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#10410 closed defect (fixed)

KeyError in structure-association chain list

Reported by:	d.ng@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Sequence	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Using modeller to model missing structures

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0004.cxs

Log from Wed Dec 27 23:13:03 2023UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0002.cxs

Log from Wed Dec 27 21:11:39 2023UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/SASDB38_fit3_model1.pdb

Summary of feedback from opening /Users/derekng/Dropbox/data-
shared/business/derekng/clients/invivo-redNucleus/2023/complement-
pathway/models/c1/source/SASDB38_fit3_model1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK File generated by Swiss-PdbViewer 4.00b0  
  
Ignored bad PDB record found on line 2  
REMARK http://www.expasy.org/spdbv/  
  
Ignored bad PDB record found on line 22  
REMARK Corresponds to Suppl Fig 4b in pubmed id 28104818  
  
Ignored bad PDB record found on line 23  
REMARK Project description: C1  
  
Ignored bad PDB record found on line 24  
REMARK j: 85 T: 0.717E-03 Suc: 91 Eva: 5926956 CPU: 0.509E+06 F:16.3033 Pen:
14.0001  
  
2736 messages similar to the above omitted  
  
Chain information for SASDB38_fit3_model1.pdb #1  
---  
Chain | Description  
A E I | No description available  
B F J | No description available  
C G K | No description available  
D H L | No description available  
M | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
  

> select /A:25-65

1284 atoms, 1296 bonds, 206 residues, 1 model selected  

> select /E:25-65

1284 atoms, 1296 bonds, 206 residues, 1 model selected  

> select /I:25-65

1284 atoms, 1296 bonds, 206 residues, 1 model selected  

> select /B:62-91

942 atoms, 954 bonds, 148 residues, 1 model selected  

> select /F:62-91

942 atoms, 954 bonds, 148 residues, 1 model selected  

> select /J:62-91

942 atoms, 954 bonds, 148 residues, 1 model selected  

> select /C:88-114

798 atoms, 806 bonds, 134 residues, 1 model selected  

> select /G:88-114

798 atoms, 806 bonds, 134 residues, 1 model selected  

> select /K:88-114

798 atoms, 806 bonds, 134 residues, 1 model selected  

> select /D:1112-1245

6112 atoms, 6252 bonds, 772 residues, 1 model selected  

> select /H:1112-1245

6112 atoms, 6252 bonds, 772 residues, 1 model selected  

> select /L:1112-1245

6112 atoms, 6252 bonds, 772 residues, 1 model selected  

> select /M:17-291

4360 atoms, 4486 bonds, 550 residues, 1 model selected  

> select clear

> hide atoms

> show cartoons

> select /M:17-291

4360 atoms, 4486 bonds, 550 residues, 1 model selected  

> select clear

Drag select of 1 residues  

> show sel atoms

> hide sel atoms

> select clear

> select /M:17-291

4360 atoms, 4486 bonds, 550 residues, 1 model selected  

> select /O:292-684

6078 atoms, 6238 bonds, 786 residues, 1 model selected  

> select /M:17-291

4360 atoms, 4486 bonds, 550 residues, 1 model selected  

> hide sel cartoons

> select /O:292-684

6078 atoms, 6238 bonds, 786 residues, 1 model selected  

> hide sel cartoons

> select /P:22-189

2666 atoms, 2744 bonds, 336 residues, 1 model selected  

> hide sel cartoons

> select /Q:190-306

1896 atoms, 1944 bonds, 234 residues, 1 model selected  

> hide sel cartoons

> select /R:307-702

6326 atoms, 6490 bonds, 792 residues, 1 model selected  

> hide sel cartoons

> color sel white

> select clear

> color white

> select clear

Drag select of 6 residues  

> select up

1308 atoms, 1320 bonds, 210 residues, 1 model selected  
Drag select of 7 residues  

> select up

1308 atoms, 1320 bonds, 210 residues, 1 model selected  

> select clear

[Repeated 3 time(s)]Drag select of 1 residues  

> select up

1308 atoms, 1320 bonds, 210 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /I

Alignment identifier is 1/I  

> select /I:25

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select /I:25-29

74 atoms, 74 bonds, 10 residues, 1 model selected  

> select /I:25

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select /I:25-47

684 atoms, 688 bonds, 110 residues, 1 model selected  

> select /I:48

42 atoms, 36 bonds, 6 residues, 1 model selected  

> select /I:48-54

272 atoms, 270 bonds, 42 residues, 1 model selected  

> select /I:59

52 atoms, 46 bonds, 6 residues, 1 model selected  

> select /I:25-59

1136 atoms, 1146 bonds, 182 residues, 1 model selected  
Drag select of 2717 residues  

> select up

22068 atoms, 22542 bonds, 2910 residues, 1 model selected  

> select up

49238 atoms, 50348 bonds, 6538 residues, 1 model selected  

> select down

22068 atoms, 22542 bonds, 2910 residues, 1 model selected  
Drag select of 407 residues  

> select up

3971 atoms, 4054 bonds, 533 residues, 1 model selected  

> select up

3993 atoms, 4077 bonds, 536 residues, 1 model selected  

> select up

7036 atoms, 7190 bonds, 920 residues, 1 model selected  

> select up

49238 atoms, 50348 bonds, 6538 residues, 1 model selected  

> select down

7036 atoms, 7190 bonds, 920 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]Drag select of 3 residues  

> select up

1308 atoms, 1320 bonds, 210 residues, 1 model selected  

> select /I:33,59

102 atoms, 92 bonds, 12 residues, 1 model selected  

> select /I:33,33,34-59

1000 atoms, 1008 bonds, 162 residues, 1 model selected  

> select /I:59

52 atoms, 46 bonds, 6 residues, 1 model selected  

> select /I:25-59

1136 atoms, 1146 bonds, 182 residues, 1 model selected  

> select clear

Drag select of 2 residues  

> select up

1308 atoms, 1320 bonds, 210 residues, 1 model selected  

> select clear

> help help:user

> sequence align #1/I,P02747

Must specify 2 or more protein sequences  
Fetching compressed P02747 UniProt info from
https://www.uniprot.org/uniprot/P02747.xml  

> sequence align P02747,#1/I

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain I with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: ZVHKXLBNQQLG2NAU  

> select /A,E,I:31

48 atoms, 36 bonds, 12 residues, 1 model selected  

> select /A,E,I:31-65

3582 atoms, 3612 bonds, 582 residues, 1 model selected  

> select clear

> sequence associate /I 1:1

Disassociated SASDB38_fit3_model1.pdb chain I from chain I  
Associated SASDB38_fit3_model1.pdb chain I to P02747 with 145 mismatches
and/or gaps  

> select /I:31

16 atoms, 12 bonds, 4 residues, 1 model selected  

> select /I:31-65

1194 atoms, 1204 bonds, 194 residues, 1 model selected  

> select /I:31

16 atoms, 12 bonds, 4 residues, 1 model selected  

> select /I:31-32

46 atoms, 42 bonds, 8 residues, 1 model selected  

> select /I:31

16 atoms, 12 bonds, 4 residues, 1 model selected  

> select /I:31-36

196 atoms, 194 bonds, 32 residues, 1 model selected  

> select #1/I:75-100

Nothing selected  

> sequence associate /I 1:2

Disassociated SASDB38_fit3_model1.pdb chain I from P02747  
Associated SASDB38_fit3_model1.pdb chain I to chain I with 0 mismatches  

> select #1/I:75-100

Nothing selected  

> select #1/I:75-100

Nothing selected  

> select #1/I:75

Nothing selected  

> select #1/I:

Expected an objects specifier or a keyword  

> select #1/I:1

Nothing selected  

> select #1/I

1308 atoms, 1320 bonds, 210 residues, 1 model selected  

> select #1/I:28

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select #1/I:28-29

24 atoms, 24 bonds, 4 residues, 1 model selected  

> select /I:67

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select
> /I:25-33,33,34,34,35,35,36,36,37,37,38,38,39,39,40,40,41,41,42,42,43,43,44,44,45,45,46,46,47,47,48,48,49,49,50,50,51,51,52,52,53,53,54,54,55,55,56,56,57,57,58,58,59,59-67

1308 atoms, 1320 bonds, 210 residues, 1 model selected  

> select /I:25

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select
> /I:25-33,33,34,34,35,35,36,36,37,37,38,38,39,39,40,40,41,41,42,42,43,43,44,44,45,45,46,46,47,47,48,48,49,49,50,50,51,51,52,52,53,53,54,54,55,55,56,56,57-59

1136 atoms, 1146 bonds, 182 residues, 1 model selected  

> select /I:25

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select /I:25-29

74 atoms, 74 bonds, 10 residues, 1 model selected  

> select /I:25

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select /I:25-42

504 atoms, 504 bonds, 80 residues, 1 model selected  

> select /I:25

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select /I:25-35

258 atoms, 258 bonds, 38 residues, 1 model selected  

> select /I:41

46 atoms, 40 bonds, 6 residues, 1 model selected  

> select /I:41-44

162 atoms, 158 bonds, 24 residues, 1 model selected  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/c1q_1.pdb

Chain information for c1q_1.pdb #2  
---  
Chain | Description  
A | No description available  
  
Associated c1q_1.pdb chain A to chain I with 0 mismatches  

> hide #2 models

> show #2 models

> close #2

> close #1

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/SASDB38_fit3_model1.pdb

Summary of feedback from opening /Users/derekng/Dropbox/data-
shared/business/derekng/clients/invivo-redNucleus/2023/complement-
pathway/models/c1/source/SASDB38_fit3_model1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK File generated by Swiss-PdbViewer 4.00b0  
  
Ignored bad PDB record found on line 2  
REMARK http://www.expasy.org/spdbv/  
  
Ignored bad PDB record found on line 22  
REMARK Corresponds to Suppl Fig 4b in pubmed id 28104818  
  
Ignored bad PDB record found on line 23  
REMARK Project description: C1  
  
Ignored bad PDB record found on line 24  
REMARK j: 85 T: 0.717E-03 Suc: 91 Eva: 5926956 CPU: 0.509E+06 F:16.3033 Pen:
14.0001  
  
2736 messages similar to the above omitted  
  
Chain information for SASDB38_fit3_model1.pdb #1  
---  
Chain | Description  
A E I | No description available  
B F J | No description available  
C G K | No description available  
D H L | No description available  
M | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
  
Associated SASDB38_fit3_model1.pdb chain A to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain I with 0 mismatches  

> hide atoms

> show cartoons

> color white

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0001.cxs

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/1.pdb

Chain information for 1.pdb #2  
---  
Chain | Description  
A | No description available  
  
Associated 1.pdb chain A to chain I with 0 mismatches  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  
Fetching compressed P02745 UniProt info from
https://www.uniprot.org/uniprot/P02745.xml  

> sequence align P02745,#2/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain A with 0 mismatches  
Associated 1.pdb chain A to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: ZHIM3ZD679W971AV  

> rename #2 "c1q_A (n-term).pdb"

> select add #2

234 atoms, 234 bonds, 35 residues, 1 model selected  

> select clear

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/grouped/c1q_A_n_term.pdb models #2 relModel #1

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/grouped/c1q_A_n_term.pdb

Chain information for c1q_A_n_term.pdb #2  
---  
Chain | Description  
A | No description available  
  
Associated c1q_A_n_term.pdb chain A to P02745 with 0 mismatches  

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/2.pdb

Chain information for 2.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence align P02745,#2/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain A with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain A with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain A with 15 mismatches  
Associated 2.pdb chain A to chain A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: AGY02F5B94T9R7WC  
Fetching compressed P02746 UniProt info from
https://www.uniprot.org/uniprot/P02746.xml  

> sequence align P02746,#2/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain A with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain A with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain A with 15 mismatches  
Associated 2.pdb chain A to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: M717PX1X8W9T1DNY  

> sequence align P02747,#2/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain A with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain A with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain A with 15 mismatches  
Associated 2.pdb chain A to chain A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: C751SE1M4IBIRM98  

> sequence align P02745,#2/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain A with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain A with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain A with 15 mismatches  
Associated 2.pdb chain A to chain A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 4KUB2VE0BC4RJQ1M  

> sequence align P02746,#2/A

Alignment identifier is 2  
Associated SASDB38_fit3_model1.pdb chain A to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain A with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain A with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain A with 15 mismatches  
Associated 2.pdb chain A to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Webservices job id: PEEVN351KOLVV4I3  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/grouped/c1q_B_n_term.pdb models #2 relModel #1

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/3.pdb

Chain information for 3.pdb #2  
---  
Chain | Description  
A | No description available  
  

> sequence align P02746,#2/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain A with 0 mismatches  
Associated 3.pdb chain A to chain A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: GUN56JDWRZWZD51P  

> sequence align P02747,#2/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain A with 0 mismatches  
Associated 3.pdb chain A to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: DT0E93XLMO2DVEBB  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/grouped/c1q_C_n_term.pdb models #2 relModel #1

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/4.pdb

Chain information for 4.pdb #2  
---  
Chain | Description  
B | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/B

Alignment identifier is 2/B  

> select #2/B:62

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/B:62-65

25 atoms, 24 bonds, 4 residues, 1 model selected  

> select #2/B:62

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/B:62-77

247 atoms, 248 bonds, 36 residues, 1 model selected  

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/4_a.pdb

Chain information for 4_a.pdb #2  
---  
Chain | Description  
B | No description available  
  

> sequence align P02745,#2/B

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain B with 0 mismatches  
Associated 4_a.pdb chain B to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: W7YIMCKC67K4DS50  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/grouped/c1q_A_collagen_pre.pdb models #2
> relModel #1

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/4_b.pdb

Chain information for 4_b.pdb #2  
---  
Chain | Description  
B | No description available  
  

> sequence align P02746,#2/B

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain B with 11 mismatches  
Associated 4_b.pdb chain B to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: HECPDU4T0LVOCM4W  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/grouped/c1q_B_collagen_pre.pdb models #2
> relModel #1

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/4_c.pdb

Chain information for 4_c.pdb #2  
---  
Chain | Description  
B | No description available  
  

> sequence align P02747,#2/B

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain B with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain B with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain B with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain B with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain B with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain B with 10 mismatches  
Associated 4_c.pdb chain B to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: T4VAJ4E7CLHZVX3S  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/grouped/c1q_C_collagen_pre.pdb models #2
> relModel #1

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/5.pdb

Chain information for 5.pdb #2  
---  
Chain | Description  
C | No description available  
  

> sequence align P02745,#2/C

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain C with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain C with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain C with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain C with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain C with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain C with 0 mismatches  
Associated 5.pdb chain C to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: J14Z1ZQ7X7OI7YPO  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/grouped/c1q_A_collagen_post.pdb models #2
> relModel #1

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/6.pdb

Chain information for 6.pdb #2  
---  
Chain | Description  
C | No description available  
  

> sequence align P02746,#2/C

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain C with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain C with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain C with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain C with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain C with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain C with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain C with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain C with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain C with 0 mismatches  
Associated 6.pdb chain C to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: X70H5VIGGMFJL1RI  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/grouped/c1q_B_collagen_post.pdb models #2
> relModel #1

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/7.pdb

Chain information for 7.pdb #2  
---  
Chain | Description  
C | No description available  
  

> sequence align P02747,#2/C

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain C with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain C with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain C with 0 mismatches  
Associated 7.pdb chain C to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: DNXPX5JASAEBB6PA  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/grouped/c1q_C_collagen_post.pdb models #2
> relModel #1

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/8.pdb

Chain information for 8.pdb #2  
---  
Chain | Description  
D | No description available  
  

> sequence align P02745,#2/D

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated 8.pdb chain D to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: XRD6RL3N631SRGLK  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/grouped/c1q_A_collagen_c_term.pdb models #2
> relModel #1

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/9.pdb

Chain information for 9.pdb #2  
---  
Chain | Description  
D | No description available  
  

> sequence align P02746,#2/D

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain D with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain D with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain D with 0 mismatches  
Associated 9.pdb chain D to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 1G4GTA4S09OGONEL  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/grouped/c1q_B_collagen_c_term.pdb models #2
> relModel #1

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/10.pdb

Chain information for 10.pdb #2  
---  
Chain | Description  
D | No description available  
  

> sequence align P02747,#2/D

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain D with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain D with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain D with 0 mismatches  
Associated 10.pdb chain D to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 4UJEPI9UPEGINRT0  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/grouped/c1q_C_collagen_c_term.pdb models #2
> relModel #1

> close #2

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_A_n_term.pdb

Chain information for c1q_A_n_term.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_A_collagen_pre.pdb

Chain information for c1q_A_collagen_pre.pdb #3  
---  
Chain | Description  
B | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_A_collagen_post.pdb

Chain information for c1q_A_collagen_post.pdb #4  
---  
Chain | Description  
C | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_A_collagen_c_term.pdb

Chain information for c1q_A_collagen_c_term.pdb #5  
---  
Chain | Description  
D | No description available  
  

> ui tool show "Change Chain IDs"

> select add #2

234 atoms, 234 bonds, 35 residues, 1 model selected  

> select add #3

398 atoms, 400 bonds, 61 residues, 2 models selected  

> select subtract #2

164 atoms, 166 bonds, 26 residues, 1 model selected  

> changechains sel A

Chain IDs of 26 residues changed  

> select subtract #3

Nothing selected  

> select add #4

136 atoms, 136 bonds, 22 residues, 1 model selected  

> changechains sel A

Chain IDs of 22 residues changed  

> select subtract #4

Nothing selected  

> select add #5

1036 atoms, 1060 bonds, 130 residues, 1 model selected  

> changechains sel A

Chain IDs of 130 residues changed  

> select subtract #5

Nothing selected  

> combine #2,#3,#4,#5

Expected a keyword  

> combine #2,3,4,5

Remapping chain ID 'A' in c1q_A_collagen_pre.pdb #3 to 'B'  
Remapping chain ID 'A' in c1q_A_collagen_post.pdb #4 to 'C'  
Remapping chain ID 'A' in c1q_A_collagen_c_term.pdb #5 to 'D'  

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> hide #!1 models

> select add #6

1570 atoms, 1596 bonds, 213 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel A

Chain IDs of 178 residues changed  

> select clear

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0002.cxs

——— End of log from Wed Dec 27 21:11:39 2023 ———

opened ChimeraX session  

> close #2-6

> open /Users/derekng/Downloads/model_01.pdb

model_01.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model_01.pdb #2  
---  
Chain | Description  
A | No description available  
  

> sequence align P02745,#2/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated model_01.pdb chain A to chain A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 0QHHC94FPAH614VQ  

> select #2/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:1-5

37 atoms, 37 bonds, 5 residues, 1 model selected  

> sequence associate #2/A 1:1

Disassociated model_01.pdb chain A from chain A  
Associated model_01.pdb chain A to P02745 with 0 mismatches  

> select #2/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:1-11

80 atoms, 80 bonds, 11 residues, 1 model selected  

> show #!1 models

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_A_A_swissmodel.pdb

c1q_A_A_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_A_A_swissmodel.pdb #3  
---  
Chain | Description  
A | No description available  
  
Associated c1q_A_A_swissmodel.pdb chain A to chain A with 0 mismatches  

> select add #2

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select add #3

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel B

Chain IDs of 220 residues changed  
Drag select of 188 residues  

> select clear

> select #1/H:1198

52 atoms, 48 bonds, 6 residues, 1 model selected  

> select up

340 atoms, 340 bonds, 44 residues, 1 model selected  

> select clear

Drag select of 382 residues  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0003.cxs

> ui tool show Matchmaker

> matchmaker #3 to #1 & sel

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker SASDB38_fit3_model1.pdb, chain H (#1) with c1q_A_A_swissmodel.pdb,
chain B (#3), sequence alignment score = 624.4  
RMSD between 128 pruned atom pairs is 0.076 angstroms; (across all 128 pairs:
0.076)  
  

> select clear

[Repeated 1 time(s)]Drag select of 3 residues  

> select up

68 atoms, 68 bonds, 10 residues, 1 model selected  

> select up

1010 atoms, 1037 bonds, 129 residues, 1 model selected  

> matchmaker #3 to #1 & sel

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker SASDB38_fit3_model1.pdb, chain H (#1) with c1q_A_A_swissmodel.pdb,
chain B (#3), sequence alignment score = 294.2  
RMSD between 104 pruned atom pairs is 0.686 angstroms; (across all 126 pairs:
2.575)  
  

> close #3

> select clear

> hide #!1 models

> rename #2 c1q_A_chainA

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0003.cxs

> show #!1 models

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainA/c1q_B_n_term.pdb

Chain information for c1q_B_n_term.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainA/c1q_B_collagen_pre.pdb

Chain information for c1q_B_collagen_pre.pdb #4  
---  
Chain | Description  
B | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainA/c1q_B_collagen_post.pdb

Chain information for c1q_B_collagen_post.pdb #5  
---  
Chain | Description  
C | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainA/c1q_B_collagen_c_term.pdb

Chain information for c1q_B_collagen_c_term.pdb #6  
---  
Chain | Description  
D | No description available  
  

> hide #!1 models

> hide #2 models

> combine #3,4,5,6

> close #3-6

> select add #7

1556 atoms, 1585 bonds, 215 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel A

Chain IDs of 180 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/processed/02/c1q_B_chainA.pdb
> models #7 relModel #1

> hide #7 models

> show #2 models

> select subtract #7

Nothing selected  

> select ::name="HYP"

888 atoms, 666 bonds, 222 residues, 2 models selected  

> select add #7

2396 atoms, 2215 bonds, 425 residues, 2 models selected  

> show #7 models

> select subtract #7

840 atoms, 630 bonds, 210 residues, 1 model selected  

> select add #1

49238 atoms, 50348 bonds, 6538 residues, 1 model selected  

> select subtract #1

Nothing selected  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_B_chainA_swissmodel.pdb

c1q_B_chainA_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_B_chainA_swissmodel.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #7 models

> show #7 models

> hide #7 models

> show #7 models

> hide #7 models

> sequence align P02746,#3/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain A with 54 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain A with 54 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain A with 54 mismatches  
Associated combination chain A to P02746 with 0 mismatches  
[Repeated 1 time(s)]Associated combination chain A to chain A with 0
mismatches  
[Repeated 1 time(s)]Associated c1q_B_chainA_swissmodel.pdb chain A to P02746
with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: X6TLX4JG82AXMB11  

> select clear

> select #1/D,H,L:1119-1121

396 atoms, 378 bonds, 48 residues, 1 model selected  

> select #1/D,H,L:1123

120 atoms, 102 bonds, 18 residues, 1 model selected  

> select #1/D,H,L:1123-1127

654 atoms, 654 bonds, 90 residues, 1 model selected  

> sequence disassociate #7/A

Disassociated combination chain A from P02746  
Disassociated combination chain A from chain A  
[Repeated 1 time(s)]Disassociated combination chain A from P02746  

> sequence disassociate #1/D

Disassociated SASDB38_fit3_model1.pdb chain D from chain A  

> sequence disassociate #1/H

Disassociated SASDB38_fit3_model1.pdb chain H from chain A  

> sequence disassociate #1/L

Disassociated SASDB38_fit3_model1.pdb chain L from chain A  

> select #3/A:32

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:32-38

50 atoms, 50 bonds, 7 residues, 1 model selected  

> show #7 models

> hide #7 models

> show #7 models

> close #3

> select clear

[Repeated 3 time(s)]

> ui tool show "Show Sequence Viewer"

> close #7

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/processed/02/c1q_B_chainA.pdb

Summary of feedback from opening /Users/derekng/Dropbox/data-
shared/business/derekng/clients/invivo-redNucleus/2023/complement-
pathway/models/c1/processed/02/c1q_B_chainA.pdb  
---  
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
records as basis for sequence.  
  
Chain information for c1q_B_chainA.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #2 models

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> sequence align P02746,#3/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain A with 74 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain A with 74 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain A with 74 mismatches  
Associated c1q_B_chainA.pdb chain A to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: HXL707BKY1Z843Z0  

> select #1/D,H,L:1163

162 atoms, 156 bonds, 18 residues, 1 model selected  

> select #1/D,H,L:1163-1165

414 atoms, 414 bonds, 54 residues, 1 model selected  

> select add #1

49238 atoms, 50348 bonds, 6538 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select ::name="HYP"

888 atoms, 666 bonds, 222 residues, 2 models selected  

> select intersect #3/A

48 atoms, 36 bonds, 12 residues, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel PRO rotLib Dunbrack

c1q_B_chainA.pdb #3/A HYP 35: phi -68.5, psi 151.6 trans  
Changed 10 bond radii  
c1q_B_chainA.pdb #!3/A HYP 38: phi -68.5, psi 151.6 trans  
Changed 10 bond radii  
c1q_B_chainA.pdb #!3/A HYP 41: phi -64.6, psi 151.5 trans  
Changed 10 bond radii  
c1q_B_chainA.pdb #!3/A HYP 53: phi -59.3, psi 151.6 trans  
Changed 10 bond radii  
c1q_B_chainA.pdb #!3/A HYP 56: phi -59.2, psi 151.6 trans  
Changed 10 bond radii  
c1q_B_chainA.pdb #!3/A HYP 65: phi -59.0, psi 151.4 trans  
Changed 10 bond radii  
c1q_B_chainA.pdb #!3/A HYP 80: phi -59.0, psi 151.5 trans  
Changed 10 bond radii  
c1q_B_chainA.pdb #!3/A HYP 83: phi -58.9, psi 151.5 trans  
Changed 10 bond radii  
c1q_B_chainA.pdb #!3/A HYP 86: phi -59.0, psi 151.5 trans  
Changed 10 bond radii  
c1q_B_chainA.pdb #!3/A HYP 101: phi -59.1, psi 151.5 trans  
Changed 10 bond radii  
c1q_B_chainA.pdb #!3/A HYP 104: phi -59.1, psi 151.6 trans  
Changed 10 bond radii  
c1q_B_chainA.pdb #!3/A HYP 107: phi -59.0, psi 151.8 trans  
Changed 10 bond radii  

> swapaa #!3/A:107 PRO criteria 1 rotLib Dunbrack

Using Dunbrack library  
c1q_B_chainA.pdb #!3/A HYP 107: phi -59.0, psi 151.8 trans  
Applying PRO rotamer (chi angles: -23.7 35.2) to c1q_B_chainA.pdb #!3/A PRO
107  

> swapaa #!3/A:104 PRO criteria 1 rotLib Dunbrack

Using Dunbrack library  
c1q_B_chainA.pdb #!3/A HYP 104: phi -59.1, psi 151.6 trans  
Applying PRO rotamer (chi angles: -23.7 35.2) to c1q_B_chainA.pdb #!3/A PRO
104  

> swapaa #!3/A:35 PRO criteria 1 rotLib Dunbrack

Using Dunbrack library  
c1q_B_chainA.pdb #!3/A HYP 35: phi -68.5, psi 151.6 trans  
Applying PRO rotamer (chi angles: 26.3 -34.2) to c1q_B_chainA.pdb #!3/A PRO 35  

> swapaa #!3/A:56 PRO criteria 1 rotLib Dunbrack

Using Dunbrack library  
c1q_B_chainA.pdb #!3/A HYP 56: phi -59.2, psi 151.6 trans  
Applying PRO rotamer (chi angles: -23.7 35.2) to c1q_B_chainA.pdb #!3/A PRO 56  

> swapaa #!3/A:65 PRO criteria 1 rotLib Dunbrack

Using Dunbrack library  
c1q_B_chainA.pdb #!3/A HYP 65: phi -59.0, psi 151.4 trans  
Applying PRO rotamer (chi angles: -23.7 35.2) to c1q_B_chainA.pdb #!3/A PRO 65  

> swapaa #!3/A:80 PRO criteria 1 rotLib Dunbrack

Using Dunbrack library  
c1q_B_chainA.pdb #!3/A HYP 80: phi -59.0, psi 151.5 trans  
Applying PRO rotamer (chi angles: -23.7 35.2) to c1q_B_chainA.pdb #!3/A PRO 80  

> swapaa #!3/A:53 PRO criteria 1 rotLib Dunbrack

Using Dunbrack library  
c1q_B_chainA.pdb #!3/A HYP 53: phi -59.3, psi 151.6 trans  
Applying PRO rotamer (chi angles: -23.7 35.2) to c1q_B_chainA.pdb #!3/A PRO 53  

> swapaa #!3/A:83 PRO criteria 1 rotLib Dunbrack

Using Dunbrack library  
c1q_B_chainA.pdb #!3/A HYP 83: phi -58.9, psi 151.5 trans  
Applying PRO rotamer (chi angles: -23.7 35.2) to c1q_B_chainA.pdb #!3/A PRO 83  

> swapaa #!3/A:41 PRO criteria 1 rotLib Dunbrack

Using Dunbrack library  
c1q_B_chainA.pdb #!3/A HYP 41: phi -64.6, psi 151.5 trans  
Applying PRO rotamer (chi angles: -23.7 35.2) to c1q_B_chainA.pdb #!3/A PRO 41  

> swapaa #!3/A:86 PRO criteria 1 rotLib Dunbrack

Using Dunbrack library  
c1q_B_chainA.pdb #!3/A HYP 86: phi -59.0, psi 151.5 trans  
Applying PRO rotamer (chi angles: -23.7 35.2) to c1q_B_chainA.pdb #!3/A PRO 86  

> swapaa #!3/A:38 PRO criteria 1 rotLib Dunbrack

Using Dunbrack library  
c1q_B_chainA.pdb #!3/A HYP 38: phi -68.5, psi 151.6 trans  
Applying PRO rotamer (chi angles: 26.3 -34.2) to c1q_B_chainA.pdb #!3/A PRO 38  

> swapaa #!3/A:101 PRO criteria 1 rotLib Dunbrack

Using Dunbrack library  
c1q_B_chainA.pdb #!3/A HYP 101: phi -59.1, psi 151.5 trans  
Applying PRO rotamer (chi angles: -23.7 35.2) to c1q_B_chainA.pdb #!3/A PRO
101  

> select add #3

1592 atoms, 1633 bonds, 215 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select ::name="HYP"

840 atoms, 630 bonds, 210 residues, 1 model selected  

> select add #1

49238 atoms, 50348 bonds, 6538 residues, 1 model selected  

> select subtract #1

Nothing selected  

> sequence align P02746,#3/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain A with 74 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain A with 74 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain A with 74 mismatches  
Associated c1q_B_chainA.pdb chain A to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 13X76KX0WXQO63FQ  

> sequence disassociate #1/D

Disassociated SASDB38_fit3_model1.pdb chain D from chain A  

> sequence disassociate #1/H

Disassociated SASDB38_fit3_model1.pdb chain H from chain A  

> sequence disassociate #1/L

Disassociated SASDB38_fit3_model1.pdb chain L from chain A  

> sequence disassociate #3/A

Disassociated c1q_B_chainA.pdb chain A from P02746  

> sequence associate #3/A 1:1

Associated c1q_B_chainA.pdb chain A to P02746 with 0 mismatches  

> select clear

[Repeated 1 time(s)]

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/processed/02/c1q_B_chainA.pdb
> models #3 relModel #1

> select add #3

1592 atoms, 1633 bonds, 215 residues, 1 model selected  

> ui tool show "Renumber Residues"

> renumber #3/A seqStart 33

0 residues renumbered  

> renumber #3/A seqStart 33

0 residues renumbered  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_B_chainA_renumbered.pdb models #3
> relModel #1

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0004.cxs

——— End of log from Wed Dec 27 23:13:03 2023 ———

opened ChimeraX session  

> rename #2 c1q_A_chainA_swissmodel

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_B_chainA_swissmodel.pdb

c1q_B_chainA_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_B_chainA_swissmodel.pdb #4  
---  
Chain | Description  
A | No description available  
  

> select subtract #3

Nothing selected  

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> sequence align #3/A,#4/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain A with 54 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain A with 54 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain A with 54 mismatches  
Associated c1q_B_chainA.pdb chain A to chain A with 0 mismatches  
Associated c1q_B_chainA_swissmodel.pdb chain A to chain A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: OLYOTC8W9O7UXTFC  

> select clear

[Repeated 1 time(s)]

> sequence disassociate #1/D

Disassociated SASDB38_fit3_model1.pdb chain D from chain A  

> sequence disassociate #1/H

Disassociated SASDB38_fit3_model1.pdb chain H from chain A  

> sequence disassociate #1/L

Disassociated SASDB38_fit3_model1.pdb chain L from chain A  

> sequence disassociate #3/A

Disassociated c1q_B_chainA.pdb chain A from chain A  

> sequence disassociate #4/A

Disassociated c1q_B_chainA_swissmodel.pdb chain A from chain A  

> sequence associate #2/A

Associated c1q_A_chainA_swissmodel chain A to chain A with 110 mismatches
and/or gaps  

> sequence disassociate #2/A

Disassociated c1q_A_chainA_swissmodel chain A from chain A  

> sequence associate #3/A 1:2

Associated c1q_B_chainA.pdb chain A to chain A with 0 mismatches  

> sequence associate #4/A 1:2

Associated c1q_B_chainA_swissmodel.pdb chain A to chain A with 0 mismatches  

> select clear

[Repeated 7 time(s)]

> select #4/A:33

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #4/A:33-37

34 atoms, 33 bonds, 5 residues, 1 model selected  

> select #4/A:53

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:1119 #4/A:53-92

262 atoms, 271 bonds, 41 residues, 2 models selected  
Clustal Omega Alignment [ID: 1] region chain A [48-87] RMSD: 0.252  
  

> select clear

[Repeated 6 time(s)]

> select #4/A:32-35

31 atoms, 30 bonds, 4 residues, 1 model selected  

> select #4/A:32-37

43 atoms, 42 bonds, 6 residues, 1 model selected  

> select clear

[Repeated 3 time(s)]

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:58

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:33-58

163 atoms, 171 bonds, 26 residues, 1 model selected  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/processed/02/temp.pdb models #3
> selectedOnly true relModel #1

> hide #3 models

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/processed/02/temp.pdb

Summary of feedback from opening /Users/derekng/Dropbox/data-
shared/business/derekng/clients/invivo-redNucleus/2023/complement-
pathway/models/c1/processed/02/temp.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 1 1 ALA
A1123 THR A1127 0  
Start residue of secondary structure not found: SHEET 2 2 1 HIS A1144 MET
A1149 0  
Start residue of secondary structure not found: SHEET 3 3 1 LYS A1159 THR
A1161 0  
Start residue of secondary structure not found: SHEET 4 4 1 GLY A1166 SER
A1176 0  
Start residue of secondary structure not found: SHEET 5 5 1 LEU A1180 GLY
A1187 0  
4 messages similar to the above omitted  
  
Chain information for temp.pdb #5  
---  
Chain | Description  
A | No description available  
  
Associated temp.pdb chain A to chain A with 0 mismatches  

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A

Alignment identifier is 5/A  

> sequence chain #4/A

Alignment identifier is 4/A  

> select #5/A:58

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5/A:58

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> show sel atoms

> style sel ball

Changed 8 atom styles  

> color sel byelement

> select #4/A:32

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #4/A:32

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> show sel atoms

> style sel ball

Changed 9 atom styles  

> color sel byelement

> select #5/A:58

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5/A:58

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #4/A:32

9 atoms, 8 bonds, 1 residue, 1 model selected  
Drag select of 17 atoms, 4 residues, 15 bonds  

> view sel

> select clear

> ui tool show "Build Structure"

> select #5/A:58@C

1 atom, 1 residue, 1 model selected  

> select add #4/A:32@N

2 atoms, 2 residues, 2 models selected  

> build join peptide sel length 1.33 omega 180 phi -120 move C

> select add #4

1611 atoms, 1655 bonds, 218 residues, 1 model selected  

> select clear

> view

> show #3 models

> select add #4

1611 atoms, 1655 bonds, 218 residues, 1 model selected  

> select subtract #4

Nothing selected  

> hide #3 models

> show #3 models

> select #4/A:47

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

591 atoms, 613 bonds, 90 residues, 1 model selected  

> select down

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #4

1611 atoms, 1655 bonds, 218 residues, 1 model selected  

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #4/A

Alignment identifier is 4/A  

> select #4/A:58

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/A:33-58

163 atoms, 171 bonds, 26 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> sequence associate #2/A

Associated c1q_A_chainA_swissmodel chain A to chain A with 136 mismatches
and/or gaps  

> sequence disassociate #4/A

Disassociated c1q_B_chainA_swissmodel.pdb chain A from chain A  

> sequence disassociate #2/A

Disassociated c1q_A_chainA_swissmodel chain A from chain A  

> sequence associate #3/A

Associated c1q_B_chainA.pdb chain A to chain A with 0 mismatches  

> sequence disassociate #3/A

Disassociated c1q_B_chainA.pdb chain A from chain A  

> sequence associate #4/A

Associated c1q_B_chainA_swissmodel.pdb chain A to chain A with 0 mismatches  

> sequence associate #3/A

Associated c1q_B_chainA.pdb chain A to chain A with 0 mismatches  

> sequence disassociate #4/A

Disassociated c1q_B_chainA_swissmodel.pdb chain A from chain A  

> sequence associate #2/A

Associated c1q_A_chainA_swissmodel chain A to chain A with 136 mismatches
and/or gaps  

> sequence disassociate #3/A

Disassociated c1q_B_chainA.pdb chain A from chain A  

> sequence associate #1/R

Associated SASDB38_fit3_model1.pdb chain R to chain A with 422 mismatches
and/or gaps  

> sequence disassociate #2/A

Disassociated c1q_A_chainA_swissmodel chain A from chain A  

> sequence disassociate #1/R

Disassociated SASDB38_fit3_model1.pdb chain R from chain A  

> sequence associate #4/A

Associated c1q_B_chainA_swissmodel.pdb chain A to chain A with 0 mismatches  

> select #4/A:58

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/A:33-58

163 atoms, 171 bonds, 26 residues, 1 model selected  

> sequence align
> QLSCTGPPAIPGIPGIPGTPGPDGQPGTPGIKGEKGLPGLAGDHGEFGEKGDPGIPGNPGKVGPKGPMGPKGGPGAPGAPGPKGESGDYKATQKIAFSATRTINVPLRRDQTIRFDHVITNMNNNYEPRSGKFTCKVPGLYYFTYHASSRGNLCVNLMRGRERAQKVVTFCDYAYNTFQVTTGGMVLKLEQGENVFLQATDKNSLLGMEGANSIFSGFLLFPDMEA,#4/A

Alignment identifier is 1  
Associated c1q_B_chainA.pdb chain A to chain A with 0 mismatches  
Associated c1q_B_chainA_swissmodel.pdb chain A to chain A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 63JIIQG9ZBFMHOU1  

> select clear

[Repeated 3 time(s)]

> select #4/A:104-105

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #4/A:104-111

61 atoms, 62 bonds, 8 residues, 1 model selected  

> select #4/A:91

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #4/A:91-112

149 atoms, 152 bonds, 22 residues, 1 model selected  

> select clear

> select #4/A:90

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> close #4

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/processed/02/temp.pdb

Summary of feedback from opening /Users/derekng/Dropbox/data-
shared/business/derekng/clients/invivo-redNucleus/2023/complement-
pathway/models/c1/processed/02/temp.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 1 1 ALA
A1123 THR A1127 0  
Start residue of secondary structure not found: SHEET 2 2 1 HIS A1144 MET
A1149 0  
Start residue of secondary structure not found: SHEET 3 3 1 LYS A1159 THR
A1161 0  
Start residue of secondary structure not found: SHEET 4 4 1 GLY A1166 SER
A1176 0  
Start residue of secondary structure not found: SHEET 5 5 1 LEU A1180 GLY
A1187 0  
4 messages similar to the above omitted  
  
Chain information for temp.pdb #4  
---  
Chain | Description  
A | No description available  
  

> select #4/A:33-58

163 atoms, 171 bonds, 26 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/A

Alignment identifier is 4/A  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_B_chainA_swissmodel.pdb

c1q_B_chainA_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_B_chainA_swissmodel.pdb #5  
---  
Chain | Description  
A | No description available  
  

> combine #4,5

Remapping chain ID 'A' in c1q_B_chainA_swissmodel.pdb #5 to 'B'  

> select add #5

1611 atoms, 1654 bonds, 218 residues, 2 models selected  

> select subtract #5

163 atoms, 171 bonds, 26 residues, 1 model selected  

> select subtract #4

Nothing selected  

> hide #3 models

> hide #4 models

> hide #5 models

> ui tool show "Show Sequence Viewer"

> sequence chain #6/A

Alignment identifier is 6/A  

> select add #6

1611 atoms, 1654 bonds, 218 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel A

Proposed chainID change conflicts with existing residue combination #6/A GLY
33  

> close #6

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/processed/02/temp.pdb

Summary of feedback from opening /Users/derekng/Dropbox/data-
shared/business/derekng/clients/invivo-redNucleus/2023/complement-
pathway/models/c1/processed/02/temp.pdb  
---  
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
records as basis for sequence.  
  
Chain information for temp.pdb #6  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #6/A

Alignment identifier is 6/A  

> close #4

> close #5

> rename #6 id #4

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_B_chainA_swissmodel.pdb

c1q_B_chainA_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_B_chainA_swissmodel.pdb #5  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A

Alignment identifier is 5/A  

> select #5/A:32

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #5/A:32

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> show sel atoms

> style sel ball

Changed 9 atom styles  

> color sel byelement

> select #4/A:58

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/A:58

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 8 atom styles  

> hide sel cartoons

> show sel atoms

> color sel byelement

> select #4/A:58@C

1 atom, 1 residue, 1 model selected  

> select #5/A:32@N

1 atom, 1 residue, 1 model selected  

> select add #4/A:58@C

2 atoms, 2 residues, 2 models selected  

> ui tool show "Build Structure"

> build join peptide sel length 1.33 omega 180 phi -120 move C

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A

Alignment identifier is 5/A  

> select add #5

1611 atoms, 1655 bonds, 218 residues, 1 model selected  

> ui tool show "Build Structure"

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A

Alignment identifier is 5/A  
Drag select of 148 residues  

> sequence associate #3/A

Associated c1q_B_chainA.pdb chain A to chain A with 0 mismatches  

> sequence disassociate #5/A

Disassociated c1q_B_chainA_swissmodel.pdb chain A from chain A  

> select clear

[Repeated 1 time(s)]

> select #3/A:41-42

11 atoms, 11 bonds, 2 residues, 1 model selected  

> select #3/A:41-49

55 atoms, 58 bonds, 9 residues, 1 model selected  

> select #3/A:35-36

12 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3/A:35-51

106 atoms, 111 bonds, 17 residues, 1 model selected  

> select #3/A:57-58

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #3/A:57-58

12 atoms, 11 bonds, 2 residues, 1 model selected  

> show #3 models

> hide #3 models

> show #3 models

> show #2 models

> close #5

> close #3

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_B_chainA_swissmodel.pdb

c1q_B_chainA_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_B_chainA_swissmodel.pdb #3  
---  
Chain | Description  
A | No description available  
  

> select #2/A

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> select add #3

3096 atoms, 3173 bonds, 412 residues, 2 models selected  

> select clear

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0004.cxs

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainA/c1q_C_n_term.pdb

Chain information for c1q_C_n_term.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainA/c1q_C_collagen_pre.pdb

Chain information for c1q_C_collagen_pre.pdb #5  
---  
Chain | Description  
B | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainA/c1q_C_collagen_post.pdb

Chain information for c1q_C_collagen_post.pdb #6  
---  
Chain | Description  
C | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainA/c1q_C_collagen_c_term.pdb

Chain information for c1q_C_collagen_c_term.pdb #7  
---  
Chain | Description  
D | No description available  
  

> hide #3 models

> hide #2 models

> combine #4,5,6,7

> hide #7 models

> hide #6 models

> hide #5 models

> hide #4 models

> select add #8

1526 atoms, 1560 bonds, 212 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel A

Chain IDs of 177 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/processed/02/c1q_C_chainA.pdb
> models #8 relModel #1

> select clear

> show #!1 models

> show #3 models

> hide #8 models

> hide #!1 models

> show #2 models

> select add #2

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> style sel sphere

Changed 1648 atom styles  

> show sel atoms

> hide sel cartoons

> select add #3

3096 atoms, 3173 bonds, 412 residues, 2 models selected  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 3096 atom styles  

> lighting soft

> lighting full

> select clear

> show #!1 models

> hide #!1 models

> show #8 models

> close #4-8

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_C_chainA_swissmodel.pdb

c1q_C_chainA_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_C_chainA_swissmodel.pdb #4  
---  
Chain | Description  
A | No description available  
  

> rename #3 c1q_B_chainA_swissmodel

> rename #4 c1q_C_chainA_swissmodel

> select clear

> select add #4

1593 atoms, 1645 bonds, 215 residues, 1 model selected  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1593 atom styles  

> select clear

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0005.cxs

> hide #2 models

> show #2 models

> show #!1 models

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/11.pdb

Chain information for 11.pdb #5  
---  
Chain | Description  
E | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/12.pdb

Chain information for 12.pdb #6  
---  
Chain | Description  
E | No description available  
  

> color #6 #db613fff

> close #6

> sequence align P02745,#5/E

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain E with 0 mismatches  
Associated c1q_A_chainA_swissmodel chain A to P02745 with 0 mismatches  
Associated 11.pdb chain E to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 6NQIZ8JJ2C37D5JZ  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_A_n_term.pdb models #5
> relModel #1

> close #5

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/12.pdb

Chain information for 12.pdb #5  
---  
Chain | Description  
E | No description available  
  

> sequence align P02746,#5/E

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain E with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain E with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain E with 15 mismatches  
Associated c1q_A_chainA_swissmodel chain A to chain E with 15 mismatches  
Associated c1q_B_chainA_swissmodel chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA_swissmodel chain A to chain E with 15 mismatches  
Associated 12.pdb chain E to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: U18IBA1EPOYS3HG0  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_B_n_term.pdb models #5
> relModel #1

> close #5

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/13.pdb

Chain information for 13.pdb #5  
---  
Chain | Description  
E | No description available  
F | No description available  
  

> select #5/E:31-65

213 atoms, 216 bonds, 35 residues, 1 model selected  

> select #5/F:62-87

164 atoms, 166 bonds, 26 residues, 1 model selected  

> sequence align P02747,#5/E

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain E with 0 mismatches  
Associated c1q_A_chainA_swissmodel chain A to chain E with 16 mismatches  
Associated c1q_B_chainA_swissmodel chain A to chain E with 16 mismatches  
Associated c1q_C_chainA_swissmodel chain A to P02747 with 0 mismatches  
Associated 13.pdb chain E to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 9EBLRR20LTU8K8VK  

> select #5/E:31-65

213 atoms, 216 bonds, 35 residues, 1 model selected  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_C_n_term.pdb models #5
> selectedOnly true relModel #1

> sequence align P02745,#5/F

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain F with 0 mismatches  
Associated c1q_A_chainA_swissmodel chain A to P02745 with 0 mismatches  
Associated c1q_B_chainA_swissmodel chain A to chain F with 11 mismatches  
Associated c1q_C_chainA_swissmodel chain A to chain F with 10 mismatches  
Associated 13.pdb chain F to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 730MQTOH0DCUCRBG  

> select #5/F:62-87

164 atoms, 166 bonds, 26 residues, 1 model selected  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_A_collagen_pre.pdb
> models #5 selectedOnly true relModel #1

> close #5

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/14.pdb

Chain information for 14.pdb #5  
---  
Chain | Description  
F | No description available  
  

> sequence align P02746,#5/F

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain F with 11 mismatches  
Associated c1q_A_chainA_swissmodel chain A to chain F with 11 mismatches  
Associated c1q_B_chainA_swissmodel chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA_swissmodel chain A to chain F with 10 mismatches  
Associated 14.pdb chain F to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: QNOIB961V9H27ICD  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_B_collagen_pre.pdb
> models #5 relModel #1

> close #5

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/15.pdb

Chain information for 15.pdb #5  
---  
Chain | Description  
F | No description available  
G | No description available  
  

> sequence align P02747,#5/F

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain F with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain F with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain F with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain F with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain F with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain F with 10 mismatches  
Associated c1q_A_chainA_swissmodel chain A to chain F with 10 mismatches  
Associated c1q_B_chainA_swissmodel chain A to chain F with 10 mismatches  
Associated c1q_C_chainA_swissmodel chain A to P02747 with 0 mismatches  
Associated 15.pdb chain F to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 4STBLS1DF86D9HQ5  

> ui tool show "Model Panel"

> select #5/F:67-91

160 atoms, 162 bonds, 25 residues, 1 model selected  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_C_collagen_pre.pdb
> models #5 selectedOnly true relModel #1

> sequence align P02745,#5/G

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain G with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain G with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain G with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain G with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain G with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain G with 0 mismatches  
Associated c1q_A_chainA_swissmodel chain A to P02745 with 0 mismatches  
Associated 15.pdb chain G to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 0F2CO1DO0FD0ARS9  

> select #5/G:88-109

136 atoms, 136 bonds, 22 residues, 1 model selected  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_A_collagen_post.pdb
> models #5 selectedOnly true relModel #1

> close #5

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/16.pdb

Chain information for 16.pdb #5  
---  
Chain | Description  
G | No description available  
  

> sequence align P02746,#5/G

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain G with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain G with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain G with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain G with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain G with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain G with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain G with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain G with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain G with 0 mismatches  
Associated c1q_B_chainA_swissmodel chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA_swissmodel chain A to chain G with 10 mismatches  
Associated 16.pdb chain G to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: O7ULL0CINM7PB9ED  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_B_collagen_post.pdb
> models #5 relModel #1

> close #5

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/17.pdb

Chain information for 17.pdb #5  
---  
Chain | Description  
G | No description available  
  

> sequence align P02747,#5/G

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain G with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain G with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain G with 0 mismatches  
Associated c1q_B_chainA_swissmodel chain A to chain G with 11 mismatches  
Associated c1q_C_chainA_swissmodel chain A to P02747 with 0 mismatches  
Associated 17.pdb chain G to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 78VLE6Z2MPXF4BWI  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_C_collagen_post.pdb
> models #5 relModel #1

> close #5

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/18.pdb

Chain information for 18.pdb #5  
---  
Chain | Description  
H | No description available  
  

> sequence align P02745,#5/H

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated c1q_A_chainA_swissmodel chain A to P02745 with 0 mismatches  
Associated 18.pdb chain H to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: KL97A7SKIBR26KEU  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_A_collagen_c_term.pdb
> models #5 relModel #1

> close #5

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/19.pdb

Chain information for 19.pdb #5  
---  
Chain | Description  
H | No description available  
  

> sequence align P02746,#5/H

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain H with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain H with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain H with 0 mismatches  
Associated c1q_B_chainA_swissmodel chain A to P02746 with 0 mismatches  
Associated 19.pdb chain H to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: KI6AEM7KW79LILNB  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_B_collagen_c_term.pdb
> models #5 relModel #1

> close #5

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/20.pdb

Chain information for 20.pdb #5  
---  
Chain | Description  
H | No description available  
  

> sequence align P02747,#5/H

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain H with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain H with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain H with 0 mismatches  
Associated c1q_C_chainA_swissmodel chain A to P02747 with 0 mismatches  
Associated 20.pdb chain H to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 9FMXSWFU3JBNYQQ8  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_C_collagen_c_term.pdb
> models #5 relModel #1

> close #5

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_A_n_term.pdb

Chain information for c1q_A_n_term.pdb #5  
---  
Chain | Description  
E | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_A_collagen_pre.pdb

Chain information for c1q_A_collagen_pre.pdb #6  
---  
Chain | Description  
F | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_A_collagen_post.pdb

Chain information for c1q_A_collagen_post.pdb #7  
---  
Chain | Description  
G | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_A_collagen_c_term.pdb

Chain information for c1q_A_collagen_c_term.pdb #8  
---  
Chain | Description  
H | No description available  
  

> hide #4 models

> hide #3 models

> hide #2 models

> show #3 models

> show #2 models

> show #4 models

> hide #!1 models

> combine #5,6,7,8

> hide #8 models

> hide #7 models

> hide #6 models

> hide #5 models

> select add #9

1570 atoms, 1596 bonds, 213 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel B

Chain IDs of 213 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainB/c1q_A_chainB.pdb models #9
> relModel #1

> close #5-9

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_B_n_term.pdb

Chain information for c1q_B_n_term.pdb #5  
---  
Chain | Description  
E | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_B_collagen_pre.pdb

Chain information for c1q_B_collagen_pre.pdb #6  
---  
Chain | Description  
F | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_B_collagen_post.pdb

Chain information for c1q_B_collagen_post.pdb #7  
---  
Chain | Description  
G | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_B_collagen_c_term.pdb

Chain information for c1q_B_collagen_c_term.pdb #8  
---  
Chain | Description  
H | No description available  
  

> combine #5,6,7,8

> select add #9

1556 atoms, 1585 bonds, 215 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel B

Chain IDs of 215 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainB/c1q_B_chainB.pdb models #9
> relModel #1

> close #5-9

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_C_n_term.pdb

Chain information for c1q_C_n_term.pdb #5  
---  
Chain | Description  
E | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_C_collagen_pre.pdb

Chain information for c1q_C_collagen_pre.pdb #6  
---  
Chain | Description  
F | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_C_collagen_post.pdb

Chain information for c1q_C_collagen_post.pdb #7  
---  
Chain | Description  
G | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainB/c1q_C_collagen_c_term.pdb

Chain information for c1q_C_collagen_c_term.pdb #8  
---  
Chain | Description  
H | No description available  
  

> combine #5,6,7,8

> select add #9

1526 atoms, 1560 bonds, 212 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel B

Chain IDs of 212 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainB/c1q_C_chainB.pdb models #9
> relModel #1

> close #5-9

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainB/c1q_A_chainB_swissmodel.pdb

c1q_A_chainB_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_A_chainB_swissmodel.pdb #5  
---  
Chain | Description  
A | No description available  
  

> rename #5 c1q_A_chainB_swissmodel

> select add #5

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel B

Chain IDs of 220 residues changed  

> select subtract #5

Nothing selected  

> select add #5

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1648 atom styles  

> select clear

> show #!1 models

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainB/c1q_B_chainB_swissmodel.pdb

c1q_B_chainB_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_B_chainB_swissmodel.pdb #6  
---  
Chain | Description  
A | No description available  
  

> rename #6 c1q_B_chainB_swissmodel

> select add #6

1448 atoms, 1483 bonds, 192 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel B

Chain IDs of 192 residues changed  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1448 atom styles  

> select clear

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainB/c1q_C_chainB_swissmodel.pdb

c1q_C_chainB_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_C_chainB_swissmodel.pdb #7  
---  
Chain | Description  
A | No description available  
  

> rename #7 c1q_C_chainB_swissmodel

> select add #7

1593 atoms, 1645 bonds, 215 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel B

Chain IDs of 215 residues changed  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1593 atom styles  

> select clear

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0006.cxs

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/21.pdb

Chain information for 21.pdb #8  
---  
Chain | Description  
I | No description available  
  

> sequence align P02745,#8/I

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain I with 0 mismatches  
Associated c1q_A_chainA_swissmodel chain A to P02745 with 0 mismatches  
Associated c1q_A_chainB_swissmodel chain B to P02745 with 0 mismatches  
Associated 21.pdb chain I to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: F5PZHLX5RZ2UKWOQ  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_A_n_term.pdb models #8
> relModel #1

> close #8

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/22.pdb

Chain information for 22.pdb #8  
---  
Chain | Description  
I | No description available  
  

> sequence align P02746,#8/I

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain I with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain I with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain I with 15 mismatches  
Associated c1q_A_chainA_swissmodel chain A to chain I with 15 mismatches  
Associated c1q_B_chainA_swissmodel chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA_swissmodel chain A to chain I with 15 mismatches  
Associated c1q_A_chainB_swissmodel chain B to chain I with 15 mismatches  
Associated c1q_B_chainB_swissmodel chain B to P02746 with 0 mismatches  
Associated c1q_C_chainB_swissmodel chain B to chain I with 15 mismatches  
Associated 22.pdb chain I to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: IFCBECO5RJ75A8YZ  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_B_n_term.pdb models #8
> relModel #1

> close #8

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/23.pdb

Chain information for 23.pdb #8  
---  
Chain | Description  
I | No description available  
  

> sequence align P02747,#8/I

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain I with 0 mismatches  
Associated c1q_A_chainA_swissmodel chain A to chain I with 16 mismatches  
Associated c1q_B_chainA_swissmodel chain A to chain I with 16 mismatches  
Associated c1q_C_chainA_swissmodel chain A to P02747 with 0 mismatches  
Associated c1q_A_chainB_swissmodel chain B to chain I with 16 mismatches  
Associated c1q_B_chainB_swissmodel chain B to chain I with 16 mismatches  
Associated c1q_C_chainB_swissmodel chain B to P02747 with 0 mismatches  
Associated 23.pdb chain I to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 9Y8NANDYY8AGPVTG  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_C_n_term.pdb models #8
> relModel #1

> close #8

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/24.pdb

Chain information for 24.pdb #8  
---  
Chain | Description  
J | No description available  
  

> sequence align P02745,#8/J

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain J with 0 mismatches  
Associated c1q_A_chainA_swissmodel chain A to P02745 with 0 mismatches  
Associated c1q_B_chainA_swissmodel chain A to chain J with 11 mismatches  
Associated c1q_C_chainA_swissmodel chain A to chain J with 10 mismatches  
Associated c1q_A_chainB_swissmodel chain B to P02745 with 0 mismatches  
Associated c1q_B_chainB_swissmodel chain B to chain J with 11 mismatches  
Associated c1q_C_chainB_swissmodel chain B to chain J with 10 mismatches  
Associated 24.pdb chain J to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: V98JJ1WUIM39L6NB  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_A_collagen_pre.pdb
> models #8 relModel #1

> close #8

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/25.pdb

Chain information for 25.pdb #8  
---  
Chain | Description  
J | No description available  
  

> sequence align P02746,#8/J

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain J with 11 mismatches  
Associated c1q_A_chainA_swissmodel chain A to chain J with 11 mismatches  
Associated c1q_B_chainA_swissmodel chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA_swissmodel chain A to chain J with 10 mismatches  
Associated c1q_A_chainB_swissmodel chain B to chain J with 11 mismatches  
Associated c1q_B_chainB_swissmodel chain B to P02746 with 0 mismatches  
Associated c1q_C_chainB_swissmodel chain B to chain J with 10 mismatches  
Associated 25.pdb chain J to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: M9A9RZ4GC2S5XOFX  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_B_collagen_pre.pdb
> models #8 relModel #1

> close #8

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/26.pdb

Chain information for 26.pdb #8  
---  
Chain | Description  
J | No description available  
  

> sequence align P02747,#8/J

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain J with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain J with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain J with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain J with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain J with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain J with 10 mismatches  
Associated c1q_A_chainA_swissmodel chain A to chain J with 10 mismatches  
Associated c1q_B_chainA_swissmodel chain A to chain J with 10 mismatches  
Associated c1q_C_chainA_swissmodel chain A to P02747 with 0 mismatches  
Associated c1q_A_chainB_swissmodel chain B to chain J with 10 mismatches  
Associated c1q_B_chainB_swissmodel chain B to chain J with 10 mismatches  
Associated c1q_C_chainB_swissmodel chain B to P02747 with 0 mismatches  
Associated 26.pdb chain J to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: SX95ZP07Z4WVHST4  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_C_collagen_pre.pdb
> models #8 relModel #1

> close #8

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/27.pdb

Chain information for 27.pdb #8  
---  
Chain | Description  
K | No description available  
  

> sequence align P02745,#8/K

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain K with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain K with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain K with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain K with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain K with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain K with 0 mismatches  
Associated c1q_A_chainA_swissmodel chain A to P02745 with 0 mismatches  
Associated c1q_A_chainB_swissmodel chain B to P02745 with 0 mismatches  
Associated 27.pdb chain K to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: V44JTBXTOB30OMPA  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_A_collagen_post.pdb
> models #8 relModel #1

> close #8

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/28.pdb

Chain information for 28.pdb #8  
---  
Chain | Description  
K | No description available  
  

> sequence align P02746,#8/K

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain K with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain K with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain K with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain K with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain K with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain K with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain K with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain K with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain K with 0 mismatches  
Associated c1q_B_chainA_swissmodel chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA_swissmodel chain A to chain K with 10 mismatches  
Associated c1q_B_chainB_swissmodel chain B to P02746 with 0 mismatches  
Associated c1q_C_chainB_swissmodel chain B to chain K with 10 mismatches  
Associated 28.pdb chain K to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 5SNBBJJPQDWUL858  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_B_collagen_post.pdb
> models #8 relModel #1

> close #8

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/29.pdb

Chain information for 29.pdb #8  
---  
Chain | Description  
K | No description available  
  

> sequence align P02747,#8/K

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain K with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain K with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain K with 0 mismatches  
Associated c1q_B_chainA_swissmodel chain A to chain K with 11 mismatches  
Associated c1q_C_chainA_swissmodel chain A to P02747 with 0 mismatches  
Associated c1q_B_chainB_swissmodel chain B to chain K with 11 mismatches  
Associated c1q_C_chainB_swissmodel chain B to P02747 with 0 mismatches  
Associated 29.pdb chain K to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: DOVJOBX428R6GPKJ  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_C_collagen_post.pdb
> models #8 relModel #1

> close #8

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/30.pdb

Chain information for 30.pdb #8  
---  
Chain | Description  
L | No description available  
  

> sequence align P02745,#8/L

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated c1q_A_chainA_swissmodel chain A to P02745 with 0 mismatches  
Associated c1q_A_chainB_swissmodel chain B to P02745 with 0 mismatches  
Associated 30.pdb chain L to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 018SL4XTUHUG5IR1  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_A_collagen_c_term.pdb
> models #8 relModel #1

> close #8

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/31.pdb

Chain information for 31.pdb #8  
---  
Chain | Description  
L | No description available  
  

> sequence align P02746,#8/L

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain L with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain L with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain L with 0 mismatches  
Associated c1q_B_chainA_swissmodel chain A to P02746 with 0 mismatches  
Associated c1q_B_chainB_swissmodel chain B to P02746 with 0 mismatches  
Associated 31.pdb chain L to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 21S2HIHCUQE033PJ  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_B_collagen_c_term.pdb
> models #8 relModel #1

> close #8

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/32.pdb

Chain information for 32.pdb #8  
---  
Chain | Description  
L | No description available  
  

> sequence align P02747,#8/L

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain L with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain L with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain L with 0 mismatches  
Associated c1q_C_chainA_swissmodel chain A to P02747 with 0 mismatches  
Associated c1q_C_chainB_swissmodel chain B to P02747 with 0 mismatches  
Associated 32.pdb chain L to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: WGYWB3CROO0SW0SA  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_C_collagen_c_term.pdb
> models #8 relModel #1

> close #8

> hide #!1 models

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_A_n_term.pdb

Chain information for c1q_A_n_term.pdb #8  
---  
Chain | Description  
I | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_A_collagen_pre.pdb

Chain information for c1q_A_collagen_pre.pdb #9  
---  
Chain | Description  
J | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_A_collagen_post.pdb

Chain information for c1q_A_collagen_post.pdb #10  
---  
Chain | Description  
K | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_A_collagen_c_term.pdb

Chain information for c1q_A_collagen_c_term.pdb #11  
---  
Chain | Description  
L | No description available  
  

> combine #8,9,10,11

> select add #12

1570 atoms, 1596 bonds, 213 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel C

Chain IDs of 213 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainC/c1q_A_chainC.pdb models #12
> relModel #1

> close #8-12

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_B_n_term.pdb

Chain information for c1q_B_n_term.pdb #8  
---  
Chain | Description  
I | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_B_collagen_pre.pdb

Chain information for c1q_B_collagen_pre.pdb #9  
---  
Chain | Description  
J | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_B_collagen_post.pdb

Chain information for c1q_B_collagen_post.pdb #10  
---  
Chain | Description  
K | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_B_collagen_c_term.pdb

Chain information for c1q_B_collagen_c_term.pdb #11  
---  
Chain | Description  
L | No description available  
  

> combine #8,9,10,11

> select add #12

1556 atoms, 1585 bonds, 215 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel C

Chain IDs of 215 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainC/c1q_B_chainC.pdb models #12
> relModel #1

> close #8-12

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_C_n_term.pdb

Chain information for c1q_C_n_term.pdb #8  
---  
Chain | Description  
I | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_C_collagen_pre.pdb

Chain information for c1q_C_collagen_pre.pdb #9  
---  
Chain | Description  
J | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_C_collagen_post.pdb

Chain information for c1q_C_collagen_post.pdb #10  
---  
Chain | Description  
K | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainC/c1q_C_collagen_c_term.pdb

Chain information for c1q_C_collagen_c_term.pdb #11  
---  
Chain | Description  
L | No description available  
  

> combine #8,9,10,11

> select add #12

1526 atoms, 1560 bonds, 212 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel C

Chain IDs of 212 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainC/c1q_C_chainC.pdb models #12
> relModel #1

> close #8-12

> show #!1 models

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/33.pdb

Chain information for 33.pdb #8  
---  
Chain | Description  
M | No description available  
  

> close #8

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainC/c1q_A_chainC_swissmodel.pdb

c1q_A_chainC_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_A_chainC_swissmodel.pdb #8  
---  
Chain | Description  
A | No description available  
  

> hide #!1 models

> rename #8 c1q_A_chainC_swissmodel

> select add #8

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel C

Chain IDs of 220 residues changed  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1648 atom styles  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainC/c1q_B_chainC_swissmodel.pdb

c1q_B_chainC_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_B_chainC_swissmodel.pdb #9  
---  
Chain | Description  
A | No description available  
  

> select subtract #8

Nothing selected  

> select add #9

1448 atoms, 1483 bonds, 192 residues, 1 model selected  

> hide #8 models

> show #8 models

> ui tool show "Change Chain IDs"

> changechains sel C

Chain IDs of 192 residues changed  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1448 atom styles  

> select clear

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainC/c1q_C_chainC_swissmodel.pdb

c1q_C_chainC_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_C_chainC_swissmodel.pdb #10  
---  
Chain | Description  
A | No description available  
  

> rename #9 c1q_B_chainC_swissmodel

> rename #10 c1q_C_chainC_swissmodel

> select add #10

1593 atoms, 1645 bonds, 215 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel C

Chain IDs of 215 residues changed  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1593 atom styles  

> select clear

> rename #10 c1q_C_chainC

> rename #9 c1q_B_chainC

> rename #8 c1q_A_chainC

> rename #7 c1q_C_chainB

> rename #6 c1q_B_chainB

> rename #5 c1q_A_chainB

> rename #4 c1q_C_chainA

> rename #3 c1q_B_chainA

> rename #2 c1q_A_chainA

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0007.cxs

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/34.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/35.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/36.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/37.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/38.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/39.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/40.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/41.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/42.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/43.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/44.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/45.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/46.pdb

Chain information for 34.pdb #11  
---  
Chain | Description  
O | No description available  
  
Chain information for 35.pdb #12  
---  
Chain | Description  
P | No description available  
  
Chain information for 36.pdb #13  
---  
Chain | Description  
Q | No description available  
  
Chain information for 37.pdb #14  
---  
Chain | Description  
R | No description available  
  
Chain information for 38.pdb #15  
---  
Chain | Description  
A | No description available  
  
Chain information for 39.pdb #16  
---  
Chain | Description  
A | No description available  
  
Chain information for 40.pdb #17  
---  
Chain | Description  
A | No description available  
  
Chain information for 41.pdb #18  
---  
Chain | Description  
B | No description available  
  
Chain information for 42.pdb #19  
---  
Chain | Description  
B | No description available  
  
Chain information for 43.pdb #20  
---  
Chain | Description  
B | No description available  
  
Chain information for 44.pdb #21  
---  
Chain | Description  
C | No description available  
  
Chain information for 45.pdb #22  
---  
Chain | Description  
C | No description available  
  
Chain information for 46.pdb #23  
---  
Chain | Description  
C | No description available  
  

> hide #11 models

> hide #12 models

> hide #13 models

> hide #14 models

> hide #15 models

> show #15 models

> close #11-23

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/38.pdb

Chain information for 38.pdb #11  
---  
Chain | Description  
A | No description available  
  

> sequence align P02745,#11/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain A with 0 mismatches  
Associated c1q_A_chainA chain A to P02745 with 0 mismatches  
Associated c1q_A_chainB chain B to P02745 with 0 mismatches  
Associated c1q_A_chainC chain C to P02745 with 0 mismatches  
Associated 38.pdb chain A to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: EUGTFO56KJ43DBDU  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_A_n_term.pdb models
> #11 relModel #1

> close #11

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/39.pdb

Chain information for 39.pdb #11  
---  
Chain | Description  
A | No description available  
  

> sequence align P02746,#11/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain A with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain A with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain A with 15 mismatches  
Associated c1q_A_chainA chain A to chain A with 15 mismatches  
Associated c1q_B_chainA chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA chain A to chain A with 15 mismatches  
Associated c1q_A_chainB chain B to chain A with 15 mismatches  
Associated c1q_B_chainB chain B to P02746 with 0 mismatches  
Associated c1q_C_chainB chain B to chain A with 15 mismatches  
Associated c1q_A_chainC chain C to chain A with 15 mismatches  
Associated c1q_B_chainC chain C to P02746 with 0 mismatches  
Associated c1q_C_chainC chain C to chain A with 15 mismatches  
Associated 39.pdb chain A to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: DE7F0M6BRA5Z4ZLD  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_B_n_term.pdb models
> #11 relModel #1

> close #11

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/40.pdb

Chain information for 40.pdb #11  
---  
Chain | Description  
A | No description available  
  

> sequence align P02747,#11/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain A with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain A with 0 mismatches  
Associated c1q_A_chainA chain A to chain A with 16 mismatches  
Associated c1q_B_chainA chain A to chain A with 16 mismatches  
Associated c1q_C_chainA chain A to P02747 with 0 mismatches  
Associated c1q_A_chainB chain B to chain A with 16 mismatches  
Associated c1q_B_chainB chain B to chain A with 16 mismatches  
Associated c1q_C_chainB chain B to P02747 with 0 mismatches  
Associated c1q_A_chainC chain C to chain A with 16 mismatches  
Associated c1q_B_chainC chain C to chain A with 16 mismatches  
Associated c1q_C_chainC chain C to P02747 with 0 mismatches  
Associated 40.pdb chain A to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 334HZCQTLK1824O8  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_C_n_term.pdb models
> #11 relModel #1

> close #11

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/41.pdb

Chain information for 41.pdb #11  
---  
Chain | Description  
B | No description available  
  

> sequence align P02745,#11/B

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain B with 0 mismatches  
Associated c1q_A_chainA chain A to P02745 with 0 mismatches  
Associated c1q_B_chainA chain A to chain B with 11 mismatches  
Associated c1q_C_chainA chain A to chain B with 10 mismatches  
Associated c1q_A_chainB chain B to P02745 with 0 mismatches  
Associated c1q_B_chainB chain B to chain B with 11 mismatches  
Associated c1q_C_chainB chain B to chain B with 10 mismatches  
Associated c1q_A_chainC chain C to P02745 with 0 mismatches  
Associated c1q_B_chainC chain C to chain B with 11 mismatches  
Associated c1q_C_chainC chain C to chain B with 10 mismatches  
Associated 41.pdb chain B to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: WKQTOREZFARHH080  

> ui tool show "Model Panel"

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_A_collagen_pre.pdb
> models #11 relModel #1

> close #11

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/42.pdb

Chain information for 42.pdb #11  
---  
Chain | Description  
B | No description available  
  

> sequence align P02746,#11/B

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain B with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain B with 11 mismatches  
Associated c1q_A_chainA chain A to chain B with 11 mismatches  
Associated c1q_B_chainA chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA chain A to chain B with 10 mismatches  
Associated c1q_A_chainB chain B to chain B with 11 mismatches  
Associated c1q_B_chainB chain B to P02746 with 0 mismatches  
Associated c1q_C_chainB chain B to chain B with 10 mismatches  
Associated c1q_A_chainC chain C to chain B with 11 mismatches  
Associated c1q_B_chainC chain C to P02746 with 0 mismatches  
Associated c1q_C_chainC chain C to chain B with 10 mismatches  
Associated 42.pdb chain B to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: XCNWPXJSXSO655J3  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_B_collagen_pre.pdb
> models #11 relModel #1

> close #11

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/43.pdb

Chain information for 43.pdb #11  
---  
Chain | Description  
B | No description available  
  

> sequence align P02747,#11/B

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain B with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain B with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain B with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain B with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain B with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain B with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain B with 10 mismatches  
Associated c1q_A_chainA chain A to chain B with 10 mismatches  
Associated c1q_B_chainA chain A to chain B with 10 mismatches  
Associated c1q_C_chainA chain A to P02747 with 0 mismatches  
Associated c1q_A_chainB chain B to chain B with 10 mismatches  
Associated c1q_B_chainB chain B to chain B with 10 mismatches  
Associated c1q_C_chainB chain B to P02747 with 0 mismatches  
Associated c1q_A_chainC chain C to chain B with 10 mismatches  
Associated c1q_B_chainC chain C to chain B with 10 mismatches  
Associated c1q_C_chainC chain C to P02747 with 0 mismatches  
Associated 43.pdb chain B to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: BDQYFGAN3SYZYBTE  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_C_collagen_pre.pdb
> models #11 relModel #1

> close #11

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/44.pdb

Chain information for 44.pdb #11  
---  
Chain | Description  
C | No description available  
  

> sequence align P02745,#11/C

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain C with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain C with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain C with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain C with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain C with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain C with 0 mismatches  
Associated c1q_A_chainA chain A to P02745 with 0 mismatches  
Associated c1q_A_chainB chain B to P02745 with 0 mismatches  
Associated c1q_A_chainC chain C to P02745 with 0 mismatches  
Associated 44.pdb chain C to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: F3VPUBVFQQM0J6AG  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_A_collagen_post.pdb
> models #11 relModel #1

> close #11

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/45.pdb

Chain information for 45.pdb #11  
---  
Chain | Description  
C | No description available  
  

> sequence align P02746,#11/C

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain C with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain C with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain C with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain C with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain C with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain C with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain C with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain C with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain C with 0 mismatches  
Associated c1q_B_chainA chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA chain A to chain C with 10 mismatches  
Associated c1q_B_chainB chain B to P02746 with 0 mismatches  
Associated c1q_C_chainB chain B to chain C with 10 mismatches  
Associated c1q_B_chainC chain C to P02746 with 0 mismatches  
Associated c1q_C_chainC chain C to chain C with 10 mismatches  
Associated 45.pdb chain C to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: SF2MQIR24WWK722C  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_B_collagen_post.pdb
> models #11 relModel #1

> close #11

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/46.pdb

Chain information for 46.pdb #11  
---  
Chain | Description  
C | No description available  
  

> sequence align P02747,#11/C

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain C with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain C with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain C with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain C with 0 mismatches  
Associated c1q_B_chainA chain A to chain C with 11 mismatches  
Associated c1q_C_chainA chain A to P02747 with 0 mismatches  
Associated c1q_B_chainB chain B to chain C with 11 mismatches  
Associated c1q_C_chainB chain B to P02747 with 0 mismatches  
Associated c1q_B_chainC chain C to chain C with 11 mismatches  
Associated c1q_C_chainC chain C to P02747 with 0 mismatches  
Associated 46.pdb chain C to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: OEA889U5XHNR0PKO  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_C_collagen_post.pdb
> models #11 relModel #1

> close #11

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/47.pdb

Chain information for 47.pdb #11  
---  
Chain | Description  
D | No description available  
  

> sequence align P02745,#11/D

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated c1q_A_chainA chain A to P02745 with 0 mismatches  
Associated c1q_A_chainB chain B to P02745 with 0 mismatches  
Associated c1q_A_chainC chain C to P02745 with 0 mismatches  
Associated 47.pdb chain D to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: AMGBZUS0X7ESJL35  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_A_collagen_c_term.pdb
> models #11 relModel #1

> close #11

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/48.pdb

Chain information for 48.pdb #11  
---  
Chain | Description  
D | No description available  
  

> sequence align P02746,#11/D

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain D with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain D with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain D with 0 mismatches  
Associated c1q_B_chainA chain A to P02746 with 0 mismatches  
Associated c1q_B_chainB chain B to P02746 with 0 mismatches  
Associated c1q_B_chainC chain C to P02746 with 0 mismatches  
Associated 48.pdb chain D to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 3DPTKSXXK4N6WHZ9  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_B_collagen_c_term.pdb
> models #11 relModel #1

> close #11

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/49.pdb

Chain information for 49.pdb #11  
---  
Chain | Description  
D | No description available  
  

> sequence align P02747,#11/D

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain D with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain D with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain D with 0 mismatches  
Associated c1q_C_chainA chain A to P02747 with 0 mismatches  
Associated c1q_C_chainB chain B to P02747 with 0 mismatches  
Associated c1q_C_chainC chain C to P02747 with 0 mismatches  
Associated 49.pdb chain D to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: ABC46Y936KL426S3  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_C_collagen_c_term.pdb
> models #11 relModel #1

> close #11

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_A_n_term.pdb

Chain information for c1q_A_n_term.pdb #11  
---  
Chain | Description  
A | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_A_collagen_pre.pdb

Chain information for c1q_A_collagen_pre.pdb #12  
---  
Chain | Description  
B | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_A_collagen_post.pdb

Chain information for c1q_A_collagen_post.pdb #13  
---  
Chain | Description  
C | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_A_collagen_c_term.pdb

Chain information for c1q_A_collagen_c_term.pdb #14  
---  
Chain | Description  
D | No description available  
  

> combine #11,12,13,14

> select add #15

1570 atoms, 1596 bonds, 213 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel D

Chain IDs of 83 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainD/c1q_A_chainD.pdb models #15
> relModel #1

> close #11-15

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_B_n_term.pdb

Chain information for c1q_B_n_term.pdb #11  
---  
Chain | Description  
A | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_B_collagen_pre.pdb

Chain information for c1q_B_collagen_pre.pdb #12  
---  
Chain | Description  
B | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_B_collagen_post.pdb

Chain information for c1q_B_collagen_post.pdb #13  
---  
Chain | Description  
C | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_B_collagen_c_term.pdb

Chain information for c1q_B_collagen_c_term.pdb #14  
---  
Chain | Description  
D | No description available  
  

> combine #11,12,13,14

> select add #15

1556 atoms, 1585 bonds, 215 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel D

Chain IDs of 83 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainD/c1q_B_chainD.pdb models #15
> relModel #1

> close #11-15

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_C_n_term.pdb

Chain information for c1q_C_n_term.pdb #11  
---  
Chain | Description  
A | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_C_collagen_pre.pdb

Chain information for c1q_C_collagen_pre.pdb #12  
---  
Chain | Description  
B | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_C_collagen_post.pdb

Chain information for c1q_C_collagen_post.pdb #13  
---  
Chain | Description  
C | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainD/c1q_C_collagen_c_term.pdb

Chain information for c1q_C_collagen_c_term.pdb #14  
---  
Chain | Description  
D | No description available  
  

> combine #11,12,13,14

> select add #15

1526 atoms, 1560 bonds, 212 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel D

Chain IDs of 83 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainD/c1q_C_chainD.pdb models #15
> relModel #1

> close #11-15

> select add #1

49238 atoms, 50348 bonds, 6538 residues, 1 model selected  

> select subtract #1

Nothing selected  

> show #!1 models

> view

> select H

Nothing selected  

> select clear

> select add #2

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> select add #10

3241 atoms, 3335 bonds, 435 residues, 2 models selected  

> select add #9

4689 atoms, 4818 bonds, 627 residues, 3 models selected  

> select add #8

6337 atoms, 6508 bonds, 847 residues, 4 models selected  

> select add #7

7930 atoms, 8153 bonds, 1062 residues, 5 models selected  

> select add #6

9378 atoms, 9636 bonds, 1254 residues, 6 models selected  

> select add #5

11026 atoms, 11326 bonds, 1474 residues, 7 models selected  

> select add #4

12619 atoms, 12971 bonds, 1689 residues, 8 models selected  

> select add #3

14067 atoms, 14454 bonds, 1881 residues, 9 models selected  

> color sel white

> select clear

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainD/c1q_A_chainD_swissmodel.pdb

c1q_A_chainD_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_A_chainD_swissmodel.pdb #11  
---  
Chain | Description  
A | No description available  
  

> rename #11 c1q_A_chainD

> select add #11

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel D

Chain IDs of 220 residues changed  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1648 atom styles  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainD/c1q_B_chainD_swissmodel.pdb

c1q_B_chainD_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_B_chainD_swissmodel.pdb #12  
---  
Chain | Description  
A | No description available  
  

> rename #12 c1q_B_chainD

> select subtract #11

Nothing selected  

> select add #12

1448 atoms, 1483 bonds, 192 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel D

Chain IDs of 192 residues changed  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1448 atom styles  

> select clear

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainD/c1q_C_chainD_swissmodel.pdb

c1q_C_chainD_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_C_chainD_swissmodel.pdb #13  
---  
Chain | Description  
A | No description available  
  

> rename #13 c1q_C_chainD

> select add #13

1593 atoms, 1645 bonds, 215 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel D

Chain IDs of 215 residues changed  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1593 atom styles  

> select clear

> select add #11

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> select add #12

3096 atoms, 3173 bonds, 412 residues, 2 models selected  

> select add #13

4689 atoms, 4818 bonds, 627 residues, 3 models selected  

> color sel white

> select clear

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0008.cxs

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/50.pdb

Chain information for 50.pdb #14  
---  
Chain | Description  
E | No description available  
  

> hide #!1 models

> sequence align P02745,#14/E

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain E with 0 mismatches  
Associated c1q_A_chainA chain A to P02745 with 0 mismatches  
Associated c1q_A_chainB chain B to P02745 with 0 mismatches  
Associated c1q_A_chainC chain C to P02745 with 0 mismatches  
Associated c1q_A_chainD chain D to P02745 with 0 mismatches  
Associated 50.pdb chain E to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: OBGE5H1ZP7ODHI9D  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_A_n_term.pdb models
> #14 relModel #1

> close #14

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/51.pdb

Chain information for 51.pdb #14  
---  
Chain | Description  
E | No description available  
  

> sequence align P02746,#14/E

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain E with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain E with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain E with 15 mismatches  
Associated c1q_A_chainA chain A to chain E with 15 mismatches  
Associated c1q_B_chainA chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA chain A to chain E with 15 mismatches  
Associated c1q_A_chainB chain B to chain E with 15 mismatches  
Associated c1q_B_chainB chain B to P02746 with 0 mismatches  
Associated c1q_C_chainB chain B to chain E with 15 mismatches  
Associated c1q_A_chainC chain C to chain E with 15 mismatches  
Associated c1q_B_chainC chain C to P02746 with 0 mismatches  
Associated c1q_C_chainC chain C to chain E with 15 mismatches  
Associated c1q_A_chainD chain D to chain E with 15 mismatches  
Associated c1q_B_chainD chain D to P02746 with 0 mismatches  
Associated c1q_C_chainD chain D to chain E with 15 mismatches  
Associated 51.pdb chain E to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: RN5F4HLJ37LHN5RL  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_B_n_term.pdb models
> #14 relModel #1

> close #14

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/52.pdb

Chain information for 52.pdb #14  
---  
Chain | Description  
E | No description available  
  

> sequence align P02747,#14/E

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain E with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain E with 0 mismatches  
Associated c1q_A_chainA chain A to chain E with 16 mismatches  
Associated c1q_B_chainA chain A to chain E with 16 mismatches  
Associated c1q_C_chainA chain A to P02747 with 0 mismatches  
Associated c1q_A_chainB chain B to chain E with 16 mismatches  
Associated c1q_B_chainB chain B to chain E with 16 mismatches  
Associated c1q_C_chainB chain B to P02747 with 0 mismatches  
Associated c1q_A_chainC chain C to chain E with 16 mismatches  
Associated c1q_B_chainC chain C to chain E with 16 mismatches  
Associated c1q_C_chainC chain C to P02747 with 0 mismatches  
Associated c1q_A_chainD chain D to chain E with 16 mismatches  
Associated c1q_B_chainD chain D to chain E with 16 mismatches  
Associated c1q_C_chainD chain D to P02747 with 0 mismatches  
Associated 52.pdb chain E to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: TGYLSBAYN2M42LUS  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_C_n_term.pdb models
> #14 relModel #1

> close #14

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/53.pdb

Chain information for 53.pdb #14  
---  
Chain | Description  
F | No description available  
  

> sequence align P02745,#14/F

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain F with 0 mismatches  
Associated c1q_A_chainA chain A to P02745 with 0 mismatches  
Associated c1q_B_chainA chain A to chain F with 11 mismatches  
Associated c1q_C_chainA chain A to chain F with 10 mismatches  
Associated c1q_A_chainB chain B to P02745 with 0 mismatches  
Associated c1q_B_chainB chain B to chain F with 11 mismatches  
Associated c1q_C_chainB chain B to chain F with 10 mismatches  
Associated c1q_A_chainC chain C to P02745 with 0 mismatches  
Associated c1q_B_chainC chain C to chain F with 11 mismatches  
Associated c1q_C_chainC chain C to chain F with 10 mismatches  
Associated c1q_A_chainD chain D to P02745 with 0 mismatches  
Associated c1q_B_chainD chain D to chain F with 11 mismatches  
Associated c1q_C_chainD chain D to chain F with 10 mismatches  
Associated 53.pdb chain F to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: QAA9R63RC63AE5VZ  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_A_collagen_pre.pdb
> models #14 relModel #1

> close #14

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/54.pdb

Chain information for 54.pdb #14  
---  
Chain | Description  
F | No description available  
  

> sequence align P02746,#14/F

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain F with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain F with 11 mismatches  
Associated c1q_A_chainA chain A to chain F with 11 mismatches  
Associated c1q_B_chainA chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA chain A to chain F with 10 mismatches  
Associated c1q_A_chainB chain B to chain F with 11 mismatches  
Associated c1q_B_chainB chain B to P02746 with 0 mismatches  
Associated c1q_C_chainB chain B to chain F with 10 mismatches  
Associated c1q_A_chainC chain C to chain F with 11 mismatches  
Associated c1q_B_chainC chain C to P02746 with 0 mismatches  
Associated c1q_C_chainC chain C to chain F with 10 mismatches  
Associated c1q_A_chainD chain D to chain F with 11 mismatches  
Associated c1q_B_chainD chain D to P02746 with 0 mismatches  
Associated c1q_C_chainD chain D to chain F with 10 mismatches  
Associated 54.pdb chain F to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: NJON53RPPNHMMQUC  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_B_collagen_pre.pdb
> models #14 relModel #1

> close #14

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/55.pdb

Chain information for 55.pdb #14  
---  
Chain | Description  
F | No description available  
  

> sequence align P02747,#14/F

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain F with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain F with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain F with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain F with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain F with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain F with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain F with 10 mismatches  
Associated c1q_A_chainA chain A to chain F with 10 mismatches  
Associated c1q_B_chainA chain A to chain F with 10 mismatches  
Associated c1q_C_chainA chain A to P02747 with 0 mismatches  
Associated c1q_A_chainB chain B to chain F with 10 mismatches  
Associated c1q_B_chainB chain B to chain F with 10 mismatches  
Associated c1q_C_chainB chain B to P02747 with 0 mismatches  
Associated c1q_A_chainC chain C to chain F with 10 mismatches  
Associated c1q_B_chainC chain C to chain F with 10 mismatches  
Associated c1q_C_chainC chain C to P02747 with 0 mismatches  
Associated c1q_A_chainD chain D to chain F with 10 mismatches  
Associated c1q_B_chainD chain D to chain F with 10 mismatches  
Associated c1q_C_chainD chain D to P02747 with 0 mismatches  
Associated 55.pdb chain F to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 7U624CQ3V6L2TUD7  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_C_collagen_pre.pdb
> models #14 relModel #1

> close #14

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/56.pdb

Chain information for 56.pdb #14  
---  
Chain | Description  
G | No description available  
  

> sequence align P02745,#14/G

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain G with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain G with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain G with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain G with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain G with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain G with 0 mismatches  
Associated c1q_A_chainA chain A to P02745 with 0 mismatches  
Associated c1q_A_chainB chain B to P02745 with 0 mismatches  
Associated c1q_A_chainC chain C to P02745 with 0 mismatches  
Associated c1q_A_chainD chain D to P02745 with 0 mismatches  
Associated 56.pdb chain G to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 6K3EDP8G6WKBNQ0K  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_A_collagen_post.pdb
> models #14 relModel #1

> close #14

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/57.pdb

Chain information for 57.pdb #14  
---  
Chain | Description  
G | No description available  
  

> sequence align P02746,#14/G

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain G with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain G with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain G with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain G with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain G with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain G with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain G with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain G with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain G with 0 mismatches  
Associated c1q_B_chainA chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA chain A to chain G with 10 mismatches  
Associated c1q_B_chainB chain B to P02746 with 0 mismatches  
Associated c1q_C_chainB chain B to chain G with 10 mismatches  
Associated c1q_B_chainC chain C to P02746 with 0 mismatches  
Associated c1q_C_chainC chain C to chain G with 10 mismatches  
Associated c1q_B_chainD chain D to P02746 with 0 mismatches  
Associated c1q_C_chainD chain D to chain G with 10 mismatches  
Associated 57.pdb chain G to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 27L4SHQZGDLLN495  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_B_collagen_post.pdb
> models #14 relModel #1

> close #14

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/58.pdb

Chain information for 58.pdb #14  
---  
Chain | Description  
G | No description available  
  

> sequence align P02747,#14/G

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain G with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain G with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain G with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain G with 0 mismatches  
Associated c1q_B_chainA chain A to chain G with 11 mismatches  
Associated c1q_C_chainA chain A to P02747 with 0 mismatches  
Associated c1q_B_chainB chain B to chain G with 11 mismatches  
Associated c1q_C_chainB chain B to P02747 with 0 mismatches  
Associated c1q_B_chainC chain C to chain G with 11 mismatches  
Associated c1q_C_chainC chain C to P02747 with 0 mismatches  
Associated c1q_B_chainD chain D to chain G with 11 mismatches  
Associated c1q_C_chainD chain D to P02747 with 0 mismatches  
Associated 58.pdb chain G to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: VJFFDC673IZB2CC8  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_C_collagen_post.pdb
> models #14 relModel #1

> close #14

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/59.pdb

Chain information for 59.pdb #14  
---  
Chain | Description  
H | No description available  
  

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting full

> show #!1 models

> hide #!1 models

> sequence align P02745,#14/H

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated c1q_A_chainA chain A to P02745 with 0 mismatches  
Associated c1q_A_chainB chain B to P02745 with 0 mismatches  
Associated c1q_A_chainC chain C to P02745 with 0 mismatches  
Associated c1q_A_chainD chain D to P02745 with 0 mismatches  
Associated 59.pdb chain H to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: LERIWYFFLUGQ2CX5  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_A_collagen_c_term.pdb
> models #14 relModel #1

> close #14

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/60.pdb

Chain information for 60.pdb #14  
---  
Chain | Description  
H | No description available  
  

> sequence align P02746,#14/H

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain H with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain H with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain H with 0 mismatches  
Associated c1q_B_chainA chain A to P02746 with 0 mismatches  
Associated c1q_B_chainB chain B to P02746 with 0 mismatches  
Associated c1q_B_chainC chain C to P02746 with 0 mismatches  
Associated c1q_B_chainD chain D to P02746 with 0 mismatches  
Associated 60.pdb chain H to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: JJZ5RX0COHQ3J5V2  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_B_collagen_c_term.pdb
> models #14 relModel #1

> close #14

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/61.pdb

Chain information for 61.pdb #14  
---  
Chain | Description  
H | No description available  
  

> sequence align P02747,#14/H

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain H with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain H with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain H with 0 mismatches  
Associated c1q_C_chainA chain A to P02747 with 0 mismatches  
Associated c1q_C_chainB chain B to P02747 with 0 mismatches  
Associated c1q_C_chainC chain C to P02747 with 0 mismatches  
Associated c1q_C_chainD chain D to P02747 with 0 mismatches  
Associated 61.pdb chain H to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: J3EQ2IL8U6QYBKKJ  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_C_collagen_c_term.pdb
> models #14 relModel #1

> close #14

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_A_n_term.pdb

Chain information for c1q_A_n_term.pdb #14  
---  
Chain | Description  
E | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_A_collagen_pre.pdb

Chain information for c1q_A_collagen_pre.pdb #15  
---  
Chain | Description  
F | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_A_collagen_post.pdb

Chain information for c1q_A_collagen_post.pdb #16  
---  
Chain | Description  
G | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_A_collagen_c_term.pdb

Chain information for c1q_A_collagen_c_term.pdb #17  
---  
Chain | Description  
H | No description available  
  

> combine #14,15,16,17

> select add #18

1570 atoms, 1596 bonds, 213 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel E

Chain IDs of 178 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainE/c1q_A_chainE.pdb models #18
> relModel #1

> close #14-18

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_B_n_term.pdb

Chain information for c1q_B_n_term.pdb #14  
---  
Chain | Description  
E | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_B_collagen_pre.pdb

Chain information for c1q_B_collagen_pre.pdb #15  
---  
Chain | Description  
F | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_B_collagen_post.pdb

Chain information for c1q_B_collagen_post.pdb #16  
---  
Chain | Description  
G | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_B_collagen_c_term.pdb

Chain information for c1q_B_collagen_c_term.pdb #17  
---  
Chain | Description  
H | No description available  
  

> combine #14,15,16,17

> select add #18

1556 atoms, 1585 bonds, 215 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel E

Chain IDs of 180 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainE/c1q_B_chainE.pdb models #18
> relModel #1

> close #14-18

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_C_n_term.pdb

Chain information for c1q_C_n_term.pdb #14  
---  
Chain | Description  
E | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_C_collagen_pre.pdb

Chain information for c1q_C_collagen_pre.pdb #15  
---  
Chain | Description  
F | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_C_collagen_post.pdb

Chain information for c1q_C_collagen_post.pdb #16  
---  
Chain | Description  
G | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainE/c1q_C_collagen_c_term.pdb

Chain information for c1q_C_collagen_c_term.pdb #17  
---  
Chain | Description  
H | No description available  
  

> combine #14,15,16,17

> select add #18

1526 atoms, 1560 bonds, 212 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel E

Chain IDs of 177 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainE/c1q_C_chainE.pdb models #18
> relModel #1

> close #14-18

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainE/c1q_A_chainE_swissmodel.pdb

c1q_A_chainE_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_A_chainE_swissmodel.pdb #14  
---  
Chain | Description  
A | No description available  
  

> rename #14 c1q_A_chainE

> select add #14

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel E

Chain IDs of 220 residues changed  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1648 atom styles  

> color sel white

> select subtract #14

Nothing selected  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainE/c1q_B_chainE_swissmodel.pdb

c1q_B_chainE_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_B_chainE_swissmodel.pdb #15  
---  
Chain | Description  
A | No description available  
  

> select add #15

1448 atoms, 1483 bonds, 192 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel E

Chain IDs of 192 residues changed  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1448 atom styles  

> color sel white

> select clear

> rename #15 c1q_B_chainE

> ui tool show "Show Sequence Viewer"

> sequence chain #15/E

Alignment identifier is 15/E  

> select #15/E:32

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #15/E

1448 atoms, 1483 bonds, 192 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #14/E

Alignment identifier is 14/E  

> select #14/E:3-4

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #14/E

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> select subtract #14

Nothing selected  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainE/c1q_C_chainE_swissmodel.pdb

c1q_C_chainE_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_C_chainE_swissmodel.pdb #16  
---  
Chain | Description  
A | No description available  
  

> rename #16 c1q_C_chainE

> select add #16

1593 atoms, 1645 bonds, 215 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel E

Chain IDs of 215 residues changed  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1593 atom styles  

> color sel white

> select clear

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0009.cxs

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/62.pdb

Chain information for 62.pdb #17  
---  
Chain | Description  
I | No description available  
  

> sequence align P02745,#17/I

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain I with 0 mismatches  
Associated c1q_A_chainA chain A to P02745 with 0 mismatches  
Associated c1q_A_chainB chain B to P02745 with 0 mismatches  
Associated c1q_A_chainC chain C to P02745 with 0 mismatches  
Associated c1q_A_chainD chain D to P02745 with 0 mismatches  
Associated c1q_A_chainE chain E to P02745 with 0 mismatches  
Associated 62.pdb chain I to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: RGPWGYU4DJURNARI  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_A_n_term.pdb models
> #17 relModel #1

> close #17

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/63.pdb

Chain information for 63.pdb #17  
---  
Chain | Description  
I | No description available  
  

> sequence align P02746,#17/I

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain I with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain I with 15 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain I with 15 mismatches  
Associated c1q_A_chainA chain A to chain I with 15 mismatches  
Associated c1q_B_chainA chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA chain A to chain I with 15 mismatches  
Associated c1q_A_chainB chain B to chain I with 15 mismatches  
Associated c1q_B_chainB chain B to P02746 with 0 mismatches  
Associated c1q_C_chainB chain B to chain I with 15 mismatches  
Associated c1q_A_chainC chain C to chain I with 15 mismatches  
Associated c1q_B_chainC chain C to P02746 with 0 mismatches  
Associated c1q_C_chainC chain C to chain I with 15 mismatches  
Associated c1q_A_chainD chain D to chain I with 15 mismatches  
Associated c1q_B_chainD chain D to P02746 with 0 mismatches  
Associated c1q_C_chainD chain D to chain I with 15 mismatches  
Associated c1q_A_chainE chain E to chain I with 15 mismatches  
Associated c1q_B_chainE chain E to P02746 with 0 mismatches  
Associated c1q_C_chainE chain E to chain I with 15 mismatches  
Associated 63.pdb chain I to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: EDQLS9VW8HI8OT1L  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_B_n_term.pdb models
> #17 relModel #1

> close #17

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/64.pdb

Chain information for 64.pdb #17  
---  
Chain | Description  
I | No description available  
  

> sequence align P02747,#17/I

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain I with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain I with 0 mismatches  
Associated c1q_A_chainA chain A to chain I with 16 mismatches  
Associated c1q_B_chainA chain A to chain I with 16 mismatches  
Associated c1q_C_chainA chain A to P02747 with 0 mismatches  
Associated c1q_A_chainB chain B to chain I with 16 mismatches  
Associated c1q_B_chainB chain B to chain I with 16 mismatches  
Associated c1q_C_chainB chain B to P02747 with 0 mismatches  
Associated c1q_A_chainC chain C to chain I with 16 mismatches  
Associated c1q_B_chainC chain C to chain I with 16 mismatches  
Associated c1q_C_chainC chain C to P02747 with 0 mismatches  
Associated c1q_A_chainD chain D to chain I with 16 mismatches  
Associated c1q_B_chainD chain D to chain I with 16 mismatches  
Associated c1q_C_chainD chain D to P02747 with 0 mismatches  
Associated c1q_A_chainE chain E to chain I with 16 mismatches  
Associated c1q_B_chainE chain E to chain I with 16 mismatches  
Associated c1q_C_chainE chain E to P02747 with 0 mismatches  
Associated 64.pdb chain I to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: J3XUW9JZSBPRSGYN  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_C_n_term.pdb models
> #17 relModel #1

> close #17

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/65.pdb

Chain information for 65.pdb #17  
---  
Chain | Description  
J | No description available  
  

> sequence align P02745,#17/J

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain J with 0 mismatches  
Associated c1q_A_chainA chain A to P02745 with 0 mismatches  
Associated c1q_B_chainA chain A to chain J with 11 mismatches  
Associated c1q_C_chainA chain A to chain J with 10 mismatches  
Associated c1q_A_chainB chain B to P02745 with 0 mismatches  
Associated c1q_B_chainB chain B to chain J with 11 mismatches  
Associated c1q_C_chainB chain B to chain J with 10 mismatches  
Associated c1q_A_chainC chain C to P02745 with 0 mismatches  
Associated c1q_B_chainC chain C to chain J with 11 mismatches  
Associated c1q_C_chainC chain C to chain J with 10 mismatches  
Associated c1q_A_chainD chain D to P02745 with 0 mismatches  
Associated c1q_B_chainD chain D to chain J with 11 mismatches  
Associated c1q_C_chainD chain D to chain J with 10 mismatches  
Associated c1q_A_chainE chain E to P02745 with 0 mismatches  
Associated c1q_B_chainE chain E to chain J with 11 mismatches  
Associated c1q_C_chainE chain E to chain J with 10 mismatches  
Associated 65.pdb chain J to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: K6Q2DE2G5YOGEKX8  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_A_collagen_pre.pdb
> models #17 relModel #1

> close #17

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/66.pdb

Chain information for 66.pdb #17  
---  
Chain | Description  
J | No description available  
  

> sequence align P02746,#17/J

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain J with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain J with 11 mismatches  
Associated c1q_A_chainA chain A to chain J with 11 mismatches  
Associated c1q_B_chainA chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA chain A to chain J with 10 mismatches  
Associated c1q_A_chainB chain B to chain J with 11 mismatches  
Associated c1q_B_chainB chain B to P02746 with 0 mismatches  
Associated c1q_C_chainB chain B to chain J with 10 mismatches  
Associated c1q_A_chainC chain C to chain J with 11 mismatches  
Associated c1q_B_chainC chain C to P02746 with 0 mismatches  
Associated c1q_C_chainC chain C to chain J with 10 mismatches  
Associated c1q_A_chainD chain D to chain J with 11 mismatches  
Associated c1q_B_chainD chain D to P02746 with 0 mismatches  
Associated c1q_C_chainD chain D to chain J with 10 mismatches  
Associated c1q_A_chainE chain E to chain J with 11 mismatches  
Associated c1q_B_chainE chain E to P02746 with 0 mismatches  
Associated c1q_C_chainE chain E to chain J with 10 mismatches  
Associated 66.pdb chain J to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: M731QKA74F9Q6DK6  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_B_collagen_pre.pdb
> models #17 relModel #1

> close #17

> sequence align P02747,#17/J

Missing or invalid "seqSource" argument: Expected alignment-id or sequences  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/67.pdb

Chain information for 67.pdb #17  
---  
Chain | Description  
J | No description available  
  

> sequence align P02747,#17/J

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain J with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain J with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain J with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain J with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain J with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain J with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain J with 10 mismatches  
Associated c1q_A_chainA chain A to chain J with 10 mismatches  
Associated c1q_B_chainA chain A to chain J with 10 mismatches  
Associated c1q_C_chainA chain A to P02747 with 0 mismatches  
Associated c1q_A_chainB chain B to chain J with 10 mismatches  
Associated c1q_B_chainB chain B to chain J with 10 mismatches  
Associated c1q_C_chainB chain B to P02747 with 0 mismatches  
Associated c1q_A_chainC chain C to chain J with 10 mismatches  
Associated c1q_B_chainC chain C to chain J with 10 mismatches  
Associated c1q_C_chainC chain C to P02747 with 0 mismatches  
Associated c1q_A_chainD chain D to chain J with 10 mismatches  
Associated c1q_B_chainD chain D to chain J with 10 mismatches  
Associated c1q_C_chainD chain D to P02747 with 0 mismatches  
Associated c1q_A_chainE chain E to chain J with 10 mismatches  
Associated c1q_B_chainE chain E to chain J with 10 mismatches  
Associated c1q_C_chainE chain E to P02747 with 0 mismatches  
Associated 67.pdb chain J to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: GH6QPK9HSGRQSQ10  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_C_collagen_pre.pdb
> models #17 relModel #1

> close #17

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/68.pdb

Chain information for 68.pdb #17  
---  
Chain | Description  
K | No description available  
  

> sequence align P02745,#17/K

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain A to chain K with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain K with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain K with 8 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain K with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain K with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain K with 0 mismatches  
Associated c1q_A_chainA chain A to P02745 with 0 mismatches  
Associated c1q_A_chainB chain B to P02745 with 0 mismatches  
Associated c1q_A_chainC chain C to P02745 with 0 mismatches  
Associated c1q_A_chainD chain D to P02745 with 0 mismatches  
Associated c1q_A_chainE chain E to P02745 with 0 mismatches  
Associated 68.pdb chain K to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: VXE2J6F0OMR8P6X7  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_A_collagen_post.pdb
> models #17 relModel #1

> close #17

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/69.pdb

Chain information for 69.pdb #17  
---  
Chain | Description  
K | No description available  
  

> sequence align P02746,#17/K

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain K with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain K with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain K with 11 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain K with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain K with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain K with 9 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain K with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain K with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain K with 0 mismatches  
Associated c1q_B_chainA chain A to P02746 with 0 mismatches  
Associated c1q_C_chainA chain A to chain K with 10 mismatches  
Associated c1q_B_chainB chain B to P02746 with 0 mismatches  
Associated c1q_C_chainB chain B to chain K with 10 mismatches  
Associated c1q_B_chainC chain C to P02746 with 0 mismatches  
Associated c1q_C_chainC chain C to chain K with 10 mismatches  
Associated c1q_B_chainD chain D to P02746 with 0 mismatches  
Associated c1q_C_chainD chain D to chain K with 10 mismatches  
Associated c1q_B_chainE chain E to P02746 with 0 mismatches  
Associated c1q_C_chainE chain E to chain K with 10 mismatches  
Associated 69.pdb chain K to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: Z8MZP67ZA0GUW2M8  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_B_collagen_post.pdb
> models #17 relModel #1

> close #17

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/70.pdb

Chain information for 70.pdb #17  
---  
Chain | Description  
K | No description available  
  

> sequence align P02747,#17/K

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain A to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain E to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain I to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain B to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain F to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain J to chain K with 10 mismatches  
Associated SASDB38_fit3_model1.pdb chain C to chain K with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain G to chain K with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain K to chain K with 0 mismatches  
Associated c1q_B_chainA chain A to chain K with 11 mismatches  
Associated c1q_C_chainA chain A to P02747 with 0 mismatches  
Associated c1q_B_chainB chain B to chain K with 11 mismatches  
Associated c1q_C_chainB chain B to P02747 with 0 mismatches  
Associated c1q_B_chainC chain C to chain K with 11 mismatches  
Associated c1q_C_chainC chain C to P02747 with 0 mismatches  
Associated c1q_B_chainD chain D to chain K with 11 mismatches  
Associated c1q_C_chainD chain D to P02747 with 0 mismatches  
Associated c1q_B_chainE chain E to chain K with 11 mismatches  
Associated c1q_C_chainE chain E to P02747 with 0 mismatches  
Associated 70.pdb chain K to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 6K7U2FZD147KX4MX  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_C_collagen_post.pdb
> models #17 relModel #1

> close #17

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/71.pdb

Chain information for 71.pdb #17  
---  
Chain | Description  
L | No description available  
  

> sequence align P02745,#17/L

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to P02745 with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to P02745 with 0 mismatches  
Associated c1q_A_chainA chain A to P02745 with 0 mismatches  
Associated c1q_A_chainB chain B to P02745 with 0 mismatches  
Associated c1q_A_chainC chain C to P02745 with 0 mismatches  
Associated c1q_A_chainD chain D to P02745 with 0 mismatches  
Associated c1q_A_chainE chain E to P02745 with 0 mismatches  
Associated 71.pdb chain L to P02745 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: DTYERNHIJ2SJRGFQ  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_A_collagen_c_term.pdb
> models #17 relModel #1

> close #17

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/72.pdb

Chain information for 72.pdb #17  
---  
Chain | Description  
L | No description available  
  

> sequence align P02746,#17/L

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain L with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain L with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain L with 0 mismatches  
Associated c1q_B_chainA chain A to P02746 with 0 mismatches  
Associated c1q_B_chainB chain B to P02746 with 0 mismatches  
Associated c1q_B_chainC chain C to P02746 with 0 mismatches  
Associated c1q_B_chainD chain D to P02746 with 0 mismatches  
Associated c1q_B_chainE chain E to P02746 with 0 mismatches  
Associated 72.pdb chain L to P02746 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: W6RXMDQZ1ID7W8KD  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_B_collagen_c_term.pdb
> models #17 relModel #1

> close #17

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/73.pdb

Chain information for 73.pdb #17  
---  
Chain | Description  
L | No description available  
  

> sequence align P02747,#17/L

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain D to chain L with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain H to chain L with 0 mismatches  
Associated SASDB38_fit3_model1.pdb chain L to chain L with 0 mismatches  
Associated c1q_C_chainA chain A to P02747 with 0 mismatches  
Associated c1q_C_chainB chain B to P02747 with 0 mismatches  
Associated c1q_C_chainC chain C to P02747 with 0 mismatches  
Associated c1q_C_chainD chain D to P02747 with 0 mismatches  
Associated c1q_C_chainE chain E to P02747 with 0 mismatches  
Associated 73.pdb chain L to P02747 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: ZT21SOKZ05ZIY8KC  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_C_collagen_c_term.pdb
> models #17 relModel #1

> close #17

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_A_n_term.pdb

Chain information for c1q_A_n_term.pdb #17  
---  
Chain | Description  
I | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_A_collagen_pre.pdb

Chain information for c1q_A_collagen_pre.pdb #18  
---  
Chain | Description  
J | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_A_collagen_post.pdb

Chain information for c1q_A_collagen_post.pdb #19  
---  
Chain | Description  
K | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_A_collagen_c_term.pdb

Chain information for c1q_A_collagen_c_term.pdb #20  
---  
Chain | Description  
L | No description available  
  

> combine #17,18,19,20

> select add #21

1570 atoms, 1596 bonds, 213 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel F

Chain IDs of 213 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainF/c1q_A_chainF.pdb models #21
> relModel #1

> close #17-21

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_B_n_term.pdb

Chain information for c1q_B_n_term.pdb #17  
---  
Chain | Description  
I | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_B_collagen_pre.pdb

Chain information for c1q_B_collagen_pre.pdb #18  
---  
Chain | Description  
J | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_B_collagen_post.pdb

Chain information for c1q_B_collagen_post.pdb #19  
---  
Chain | Description  
K | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_B_collagen_c_term.pdb

Chain information for c1q_B_collagen_c_term.pdb #20  
---  
Chain | Description  
L | No description available  
  

> combine #17,18,19,20

> select add #21

1556 atoms, 1585 bonds, 215 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel F

Chain IDs of 215 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainF/c1q_B_chainF.pdb models #21
> relModel #1

> close #17-21

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_C_n_term.pdb

Chain information for c1q_C_n_term.pdb #17  
---  
Chain | Description  
I | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_C_collagen_pre.pdb

Chain information for c1q_C_collagen_pre.pdb #18  
---  
Chain | Description  
J | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_C_collagen_post.pdb

Chain information for c1q_C_collagen_post.pdb #19  
---  
Chain | Description  
K | No description available  
  

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1q_chainF/c1q_C_collagen_c_term.pdb

Chain information for c1q_C_collagen_c_term.pdb #20  
---  
Chain | Description  
L | No description available  
  

> combine #17,18,19,20

> select add #21

1526 atoms, 1560 bonds, 212 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel F

Chain IDs of 212 residues changed  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainF/c1q_C_chainF.pdb models #21
> relModel #1

> close #17-21

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainF/c1q_A_chainF_swissmodel.pdb

c1q_A_chainF_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_A_chainF_swissmodel.pdb #17  
---  
Chain | Description  
A | No description available  
  

> select add #17

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel F

Chain IDs of 220 residues changed  

> rename #17 c1q_A_chainF

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1648 atom styles  

> color sel white

> select clear

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainF/c1q_B_chainF_swissmodel.pdb

c1q_B_chainF_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_B_chainF_swissmodel.pdb #18  
---  
Chain | Description  
A | No description available  
  

> rename #18 c1q_B_chainF

> select add #18

1448 atoms, 1483 bonds, 192 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel F

Chain IDs of 192 residues changed  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1448 atom styles  

> color sel white

> select clear

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1q_chainF/c1q_C_chainF_swissmodel.pdb

c1q_C_chainF_swissmodel.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for c1q_C_chainF_swissmodel.pdb #19  
---  
Chain | Description  
A | No description available  
  

> rename #19 c1q_C_chainF

> select add #19

1593 atoms, 1645 bonds, 215 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel F

Chain IDs of 215 residues changed  

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 1593 atom styles  

> color sel white

> select clear

> show #!1 models

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/modeling_0010.cxs

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/33.pdb

Chain information for 33.pdb #20  
---  
Chain | Description  
M | No description available  
  

> select add #2

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> select add #5

3296 atoms, 3380 bonds, 440 residues, 2 models selected  

> select add #17

4944 atoms, 5070 bonds, 660 residues, 3 models selected  

> select add #14

6592 atoms, 6760 bonds, 880 residues, 4 models selected  

> select add #11

8240 atoms, 8450 bonds, 1100 residues, 5 models selected  

> select add #8

9888 atoms, 10140 bonds, 1320 residues, 6 models selected  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/processed/03/c1q_A.pdb
> selectedOnly true relModel #1

> select subtract #2

8240 atoms, 8450 bonds, 1100 residues, 5 models selected  

> select subtract #5

6592 atoms, 6760 bonds, 880 residues, 4 models selected  

> select subtract #8

4944 atoms, 5070 bonds, 660 residues, 3 models selected  

> select subtract #11

3296 atoms, 3380 bonds, 440 residues, 2 models selected  

> select subtract #14

1648 atoms, 1690 bonds, 220 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #3

1448 atoms, 1483 bonds, 192 residues, 1 model selected  

> select add #6

2896 atoms, 2966 bonds, 384 residues, 2 models selected  

> select add #9

4344 atoms, 4449 bonds, 576 residues, 3 models selected  

> select add #12

5792 atoms, 5932 bonds, 768 residues, 4 models selected  

> select add #15

7240 atoms, 7415 bonds, 960 residues, 5 models selected  

> select add #18

8688 atoms, 8898 bonds, 1152 residues, 6 models selected  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/processed/03/c1q_B.pdb
> selectedOnly true relModel #1

> select subtract #3

7240 atoms, 7415 bonds, 960 residues, 5 models selected  

> select clear

> select add #4

1593 atoms, 1645 bonds, 215 residues, 1 model selected  

> select add #7

3186 atoms, 3290 bonds, 430 residues, 2 models selected  

> select add #10

4779 atoms, 4935 bonds, 645 residues, 3 models selected  

> select add #13

6372 atoms, 6580 bonds, 860 residues, 4 models selected  

> select add #16

7965 atoms, 8225 bonds, 1075 residues, 5 models selected  

> select add #19

9558 atoms, 9870 bonds, 1290 residues, 6 models selected  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/processed/03/c1q_C.pdb
> selectedOnly true relModel #1

> select clear

Fetching compressed P00736 UniProt info from
https://www.uniprot.org/uniprot/P00736.xml  

> sequence align P00736,#20/M

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain R to P00736 with 2 mismatches  
Associated SASDB38_fit3_model1.pdb chain M to chain M with 0 mismatches  
Associated 33.pdb chain M to chain M with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: LF55C53DOZ2861Y5  
Fetching compressed P09871 UniProt info from
https://www.uniprot.org/uniprot/P09871.xml  

> sequence align P09871,#20/M

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain O to P09871 with 3 mismatches  
Associated SASDB38_fit3_model1.pdb chain M to chain M with 0 mismatches  
Associated 33.pdb chain M to P09871 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: SH00X07SVJEBKXTG  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1s_chainA/cs_1.pdb models #20
> relModel #1

> close #20

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/34.pdb

Chain information for 34.pdb #20  
---  
Chain | Description  
O | No description available  
  

> close #20

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/35.pdb

Chain information for 35.pdb #20  
---  
Chain | Description  
P | No description available  
  

> close #20

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/36.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/37.pdb

Chain information for 36.pdb #20  
---  
Chain | Description  
Q | No description available  
  
Chain information for 37.pdb #21  
---  
Chain | Description  
R | No description available  
  

> close #20-21

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/74.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/75.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/76.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/77.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/78.pdb

Chain information for 74.pdb #20  
---  
Chain | Description  
M | No description available  
  
Chain information for 75.pdb #21  
---  
Chain | Description  
O | No description available  
  
Chain information for 76.pdb #22  
---  
Chain | Description  
P | No description available  
  
Chain information for 77.pdb #23  
---  
Chain | Description  
Q | No description available  
  
Chain information for 78.pdb #24  
---  
Chain | Description  
R | No description available  
  

> select add #20

2180 atoms, 2243 bonds, 275 residues, 1 model selected  

> select add #21

5219 atoms, 5362 bonds, 668 residues, 2 models selected  

> select subtract #20

3039 atoms, 3119 bonds, 393 residues, 1 model selected  

> close #20,22-24

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/33.pdb

Chain information for 33.pdb #20  
---  
Chain | Description  
M | No description available  
  

> select add #20

5219 atoms, 5362 bonds, 668 residues, 2 models selected  

> hide #!1 models

> show #!1 models

> close #21

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/34.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/35.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/36.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/37.pdb

Chain information for 34.pdb #21  
---  
Chain | Description  
O | No description available  
  
Chain information for 35.pdb #22  
---  
Chain | Description  
P | No description available  
  
Chain information for 36.pdb #23  
---  
Chain | Description  
Q | No description available  
  
Chain information for 37.pdb #24  
---  
Chain | Description  
R | No description available  
  

> select add #21

5219 atoms, 5362 bonds, 668 residues, 2 models selected  

> close #22-24

> sequence align P09871,#20/M

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain O to P09871 with 3 mismatches  
Associated SASDB38_fit3_model1.pdb chain M to chain M with 0 mismatches  
Associated 33.pdb chain M to P09871 with 0 mismatches  
Associated 34.pdb chain O to P09871 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: 29ZRMCBGJVM8D7Z9  

> sequence align P09871,#21/O

Alignment identifier is 2  
Associated SASDB38_fit3_model1.pdb chain O to chain O with 0 mismatches  
Associated 33.pdb chain M to P09871 with 0 mismatches  
Associated 34.pdb chain O to P09871 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Webservices job id: 1NVWD1KG33AL3SJA  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1s_chainA/cs_2.pdb models #21
> relModel #1

> close #20-21

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/74.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-pathway/models/c1/source/temp/75.pdb

Chain information for 74.pdb #20  
---  
Chain | Description  
M | No description available  
  
Chain information for 75.pdb #21  
---  
Chain | Description  
O | No description available  
  

> sequence align P09871,#20/M

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain O to P09871 with 3 mismatches  
Associated SASDB38_fit3_model1.pdb chain M to chain M with 0 mismatches  
Associated 74.pdb chain M to P09871 with 0 mismatches  
Associated 75.pdb chain O to P09871 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: M42Y2R6OJU1NW8SE  

> sequence align P09871,#21/O

Alignment identifier is 2  
Associated SASDB38_fit3_model1.pdb chain O to chain O with 0 mismatches  
Associated 74.pdb chain M to P09871 with 0 mismatches  
Associated 75.pdb chain O to P09871 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Webservices job id: Q5DIPJN96UXCOV77  

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1s_chainB/c1s_1.pdb models #20
> relModel #1

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1s_chainB/c1s_2.pdb models #21
> relModel #1

> close #20-21

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1s_chainA/c1s_1.pdb
> /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/01_grouped/c1s_chainA/c1s_2.pdb

Chain information for c1s_1.pdb #20  
---  
Chain | Description  
M | No description available  
  
Chain information for c1s_2.pdb #21  
---  
Chain | Description  
O | No description available  
  

> combine #20,21

> select add #22

5219 atoms, 5362 bonds, 668 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel A

Chain IDs of 668 residues changed  

> hide #!1 models

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5-19 target m

> select clear

> ui tool show "Show Sequence Viewer"

> save /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1s_chainA/c1s_chainA.pdb models #22 relModel
> #1

> close #20-22

> open /Users/derekng/Dropbox/data-shared/business/derekng/clients/invivo-
> redNucleus/2023/complement-
> pathway/models/c1/processed/02/c1s_chainA/c1s_chainA.pdb

Summary of feedback from opening /Users/derekng/Dropbox/data-
shared/business/derekng/clients/invivo-redNucleus/2023/complement-
pathway/models/c1/processed/02/c1s_chainA/c1s_chainA.pdb  
---  
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
records as basis for sequence.  
  
Chain information for c1s_chainA.pdb #20  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #20/A

Alignment identifier is 20/A  

> sequence align P09871,#20/A

Alignment identifier is 1  
Associated SASDB38_fit3_model1.pdb chain O to chain A with 0 mismatches  
Associated c1s_chainA.pdb chain A to P09871 with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: ZJ8P394Y8UX92SL7  

> select #20/A:290-291

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select #20/A:290-292

23 atoms, 22 bonds, 3 residues, 1 model selected  

> select #20/A:281-282

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #20/A:281-292

104 atoms, 107 bonds, 12 residues, 1 model selected  

> select #20/A:288

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #20/A:288-297

75 atoms, 77 bonds, 10 residues, 1 model selected  

> ui tool show "Model Loops"

> modeller refine 1:1:288-297 numModels 5 fast false adjacentFlexible 1
> protocol standard executableLocation /Library/modeller-10.4/bin/mod10.4

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker c1s_chainA.pdb, chain A (#20) with P09871, chain A (#), sequence
alignment score = 3500.2  
RMSD between 661 pruned atom pairs is 0.087 angstroms; (across all 668 pairs:
0.863)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker c1s_chainA.pdb, chain A (#20) with P09871, chain A (#), sequence
alignment score = 3493  
RMSD between 658 pruned atom pairs is 0.032 angstroms; (across all 668 pairs:
1.404)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker c1s_chainA.pdb, chain A (#20) with P09871, chain A (#), sequence
alignment score = 3507.4  
RMSD between 661 pruned atom pairs is 0.079 angstroms; (across all 668 pairs:
0.610)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker c1s_chainA.pdb, chain A (#20) with P09871, chain A (#), sequence
alignment score = 3503.8  
RMSD between 659 pruned atom pairs is 0.075 angstroms; (across all 668 pairs:
0.936)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker c1s_chainA.pdb, chain A (#20) with P09871, chain A (#), sequence
alignment score = 3503.8  
RMSD between 659 pruned atom pairs is 0.075 angstroms; (across all 668 pairs:
0.546)  
  
Associated P09871 chain A to P09871 with 0 mismatches  
[Repeated 4 time(s)]Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 717, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/common.py", line 784, in process_results  
self.caller.process_ok_models(model_info, get_pdb_model)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/common.py", line 455, in process_ok_models  
alignment.associate(models, seq=target_seq)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 391, in associate  
self._notify_observers(note_name, note_data)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 822, in _notify_observers  
recipient.alignment_notification(self.NOTE_MOD_ASSOC, (note_name, note_data))  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/tool.py", line 463, in alignment_notification  
self.associations_tool._assoc_mod(note_data)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/associations_tool.py", line 118, in _assoc_mod  
self._set_ss_data()  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/associations_tool.py", line 184, in _set_ss_data  
self.ss_chain_list.value = self.sv.alignment.associations.keys()  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/widgets.py", line 91, in value  
self.set_value(val)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 151, in set_value  
self._select_value(val)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 236, in _select_value  
val_names = set([self.value_map[v] for v in val])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 236, in <listcomp>  
val_names = set([self.value_map[v] for v in val])  
~~~~~~~~~~~~~~^^^  
KeyError: <chimerax.atomic.molobject.Chain object at 0x377301d50>  
  
KeyError:  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 236, in  
val_names = set([self.value_map[v] for v in val])  
~~~~~~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Model Number: Z11B000ENLL/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 7 days, 17 hours, 45 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component:	Unassigned → Sequence
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → KeyError in structure-association chain list

Hi David,

Thanks for reporting this problem. It happens when Modeller returns if you have used the structure-association tool of the sequence viewer. I'll see what I can do to fix it.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:2 by Eric Pettersen, 2 years ago

Resolution:	→ fixed
Status:	accepted → closed

Fixed in tomorrow's 1.8 daily build, and the upcoming 1.7.1 release, sometime in early January.

Fix: https://github.com/RBVI/ChimeraX/commit/64e0ae991de9eda4e864ec0076de0ad09b679856

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