id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10007 Session files get larger on each save drorn@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description At some point every time I'm saving a session my files get larger and larger regardless of what I have in them . The session contains no surfsce, just a few proteins that are relatively small - on the order of 200 AA. I had the same problem two years ago: refe #5139 Then I was provided with a python script to clean up some ""zombie""sequences from the session. I tried to run it on the current sessions but it doesn't work. Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs"" Log from Tue Oct 17 18:44:05 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs"" format session Log from Tue Oct 17 18:18:24 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs"" format > session Log from Tue Oct 17 14:26:21 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs"" format > session Frozen name ""ChlideX2"" not restored: nothing is selected by specifier Log from Tue Oct 17 13:50:43 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB design p_ap_p_p_ap Chl prot > interactions.cxs"" Log from Wed Aug 16 16:38:24 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB design p_ap_p_p_ap > packing.cxs"" format session Log from Wed Aug 16 15:24:32 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7pbw format mmcif fromDatabase pdb 7pbw title: Cryo-EM structure of light harvesting complex 2 from Rba. sphaeroides. [more info...] Chain information for 7pbw #1 --- Chain | Description | UniProt AA AB AC AD AE AF AG AH AI | Light-harvesting protein B-800/850 alpha chain | LHA2_RHOS4 1-50 BA BB BC BD BE BF BG BH BI | Light-harvesting protein B-800/850 beta chain | LHB2_RHOS4 5-51 Non-standard residues in 7pbw #1 --- 7OT — spheroidene ((6E,10E,12E,14E,16E,18E,20E,22E,24E,26E,28E)-31-methoxy-2,6,10,14,19,23,27,31-octamethyl- dotriaconta-2,6,10,12,14,16,18,20,22,24,26,28-dodecaene) BCL — bacteriochlorophyll A CA — calcium ion LDA — lauryl dimethylamine-N-oxide > select protein 6525 atoms, 6696 bonds, 873 residues, 1 model selected > style sel stick Changed 6525 atom styles > hide sel atoms > show sel cartoons > select helix 5310 atoms, 5427 bonds, 720 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /BA /BB /BC /BD /BE /BF /BG /BH /BI Alignment identifier is 1 > sequence chain /AA /AB /AC /AD /AE /AF /AG /AH /AI Alignment identifier is 2 ********** Deleted several thousands lines to stay within Trac limits *********** BCL 101 CED -0.262 3.902 LH2_Sphaeroides.pdb #1.1/J ALA 39 C LH2_Sphaeroides.pdb #1.1/A BCL 101 CMD -0.270 3.760 LH2_Sphaeroides.pdb #1.1/J ALA 39 O LH2_Sphaeroides.pdb #1.1/A BCL 101 CMD -0.311 3.611 LH2_Sphaeroides.pdb #1.1/J ALA 36 CA LH2_Sphaeroides.pdb #1.1/A BCL 101 CGD -0.338 3.828 LH2_Sphaeroides.pdb #1.1/J HIS 40 N LH2_Sphaeroides.pdb #1.1/A BCL 101 CMD -0.340 3.860 LH2_Sphaeroides.pdb #1.1/J ALA 39 CB LH2_Sphaeroides.pdb #1.1/A BCL 101 CMD -0.346 4.106 LH2_Sphaeroides.pdb #1.1/J PHE 32 CD1 LH2_Sphaeroides.pdb #1.1/A BCL 101 CED -0.362 4.002 LH2_Sphaeroides.pdb #1.1/J MET 35 CG LH2_Sphaeroides.pdb #1.1/A BCL 101 O1D -0.363 3.663 LH2_Sphaeroides.pdb #1.1/J PHE 32 CZ LH2_Sphaeroides.pdb #1.1/A BCL 101 O2D -0.367 3.587 LH2_Sphaeroides.pdb #1.1/J ALA 36 CA LH2_Sphaeroides.pdb #1.1/A BCL 101 O1D -0.373 3.673 32 contacts > close #2-3 > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > select add #1.2 9531 atoms, 9495 bonds, 325 pseudobonds, 1191 residues, 5 models selected > select subtract #1.2 31 atoms, 7 residues, 1 model selected > hide #!1.2 models > show #!1.2 models > select add #1.2 9531 atoms, 9495 bonds, 325 pseudobonds, 1191 residues, 5 models selected > hide #!1.2 models > show #!1.2 models > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > show #!1.1 models > select subtract #1.2 31 atoms, 7 residues, 1 model selected > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > show #!1.1 models > select #1.1 9500 atoms, 9495 bonds, 350 pseudobonds, 1184 residues, 5 models selected > select #1.2 9500 atoms, 9495 bonds, 325 pseudobonds, 1184 residues, 4 models selected > select #1.1 9500 atoms, 9495 bonds, 350 pseudobonds, 1184 residues, 5 models selected > show sel cartoons > hide sel cartoons > select #1.2 9500 atoms, 9495 bonds, 325 pseudobonds, 1184 residues, 4 models selected > show sel cartoons > select #1.2 9500 atoms, 9495 bonds, 217 pseudobonds, 1184 residues, 3 models selected > hide sel cartoons > close #1.2 > view > help help:user > combine #1.1 modelID 2 Expected a keyword > combine #1.1 > hide #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > close #1 > rename #2 LH2_Sphaeroides.pdb > hide #!4 models > select #2/A-B/J-K 2129 atoms, 2125 bonds, 228 pseudobonds, 266 residues, 5 models selected > split #2 atoms /A-B/J-K Split LH2_Sphaeroides.pdb (#2) into 2 models Chain information for LH2_Sphaeroides.pdb 1 #2.1 --- Chain | Description A B | No description available J K | No description available Chain information for LH2_Sphaeroides.pdb 2 #2.2 --- Chain | Description C D E F G H I | No description available L M N O P Q R | No description available > hide #!2.2 models > hide #!2.1 models > show #!2.1 models > show #!4 models > save ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB design p_ap_p_p_ap > refine.cxs"" > help help:user > select #4/A:21@CA,CB,CG,CD2,C4D,ND1,NE2 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/A:21@CA,CB,CG,CD2,CE1,ND1,NE2 7 atoms, 7 bonds, 1 residue, 1 model selected > align #4/A:21@CA,CB,CG,CD2,CE1,ND1,NE2 toAtoms #2.1/A:31 move atoms > matchAtomNames Missing ""matchAtomNames"" keyword's argument > align #4/A:21@CA,CB,CG,CD2,CE1,ND1,NE2 toAtoms #2.1/A:31 move atoms > matchAtomNames true Pairing dropped 0 atoms and 3 reference atoms RMSD between 7 atom pairs is 0.046 angstroms > select up 11 atoms, 11 bonds, 1 residue, 1 model selected > select #4/D#2.1/K 613 atoms, 608 bonds, 70 pseudobonds, 94 residues, 6 models selected > select #4/D@CA #2.1/K@CA 76 atoms, 54 pseudobonds, 76 residues, 4 models selected > align #4/D@CA toAtoms #2.1/K@CA move chains matchAtomNames true Pairing dropped 0 atoms and 20 reference atoms RMSD between 28 atom pairs is 4.361 angstroms > align #4/D@CA toAtoms #2.1/K:20-47@CA move chains matchAtomNames true RMSD between 28 atom pairs is 0.972 angstroms > align #4/D:21@CA,CB,CG,CD2,CE1,ND1,NE2 toAtoms #2.1/K:40 move atoms > matchAtomNames true Pairing dropped 0 atoms and 3 reference atoms RMSD between 7 atom pairs is 0.067 angstroms > select #4:1@N,C,CA 15 atoms, 10 bonds, 5 residues, 1 model selected > show sel atoms > select #4:1@N,C 10 atoms, 5 residues, 1 model selected > select #4:1@C 5 atoms, 5 residues, 1 model selected > hide sel atoms > select #4:28@C,O 10 atoms, 5 bonds, 5 residues, 1 model selected > show sel atoms > select #4/D:28@C#2.1/K:48@N 2 atoms, 2 residues, 2 models selected > ui tool show Distances > distance #4/D:28@C #2.1/K:48@N Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/D GLY 28 C and LH2_Sphaeroides.pdb 1 #2.1/K PRO 48 N: 3.877Å > select #4/E:1@N#2.1/K:49@C 2 atoms, 2 residues, 2 models selected > distance #4/E:1@N #2.1/K:49@C Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/E GLY 1 N and LH2_Sphaeroides.pdb 1 #2.1/K TRP 49 C: 12.120Å > select #4/E:28@C#4/C:1@N 2 atoms, 2 residues, 1 model selected > select #4/E:28@D#4/C:1@N 1 atom, 1 residue, 1 model selected > select #4/E:28@D#4/D:1@N 1 atom, 1 residue, 1 model selected > select #4/E:28@C#4/D:1@N 2 atoms, 2 residues, 1 model selected > distance #4/D:1@N #4/E:28@C Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/D GLY 1 N and /E GLY 28 C: 15.336Å > ~distance #4/D:1@N #4/E:28@C > select #4/E:28@C#4/C:1@N 2 atoms, 2 residues, 1 model selected > distance #4/C:1@N #4/E:28@C Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/C GLY 1 N and /E GLY 28 C: 8.966Å > select #2.1/B:41 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #4/B:1@N#2.1/B:40@C 2 atoms, 2 residues, 2 models selected > distance #4/B:1@N #2.1/B:40@C Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/B GLY 1 N and LH2_Sphaeroides.pdb 1 #2.1/B TRP 40 C: 4.651Å > select #4/B:28@C#4/A:1@N 2 atoms, 2 residues, 1 model selected > distance #4/A:1@N #4/B:28@C Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/A GLY 1 N and /B GLY 28 C: 10.907Å > select #4/A:23-28 30 atoms, 29 bonds, 5 pseudobonds, 6 residues, 2 models selected > show sel atoms > select #4/A:23-28#2.1/A:33-38 71 atoms, 69 bonds, 8 pseudobonds, 12 residues, 4 models selected > show sel atoms > save ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB design p_ap_p_p_ap refine > and connect.cxs"" > align #4/A:23-28 toAtoms #2.1/A:33-38 matchAtomNames true move atoms Pairing dropped 6 atoms and 17 reference atoms RMSD between 24 atom pairs is 0.630 angstroms > select #4/A:23-28@N,C,O,H 24 atoms, 17 bonds, 6 residues, 1 model selected > hide sel atoms > select #4/A:28@C,O 2 atoms, 1 bond, 1 residue, 1 model selected > show sel atoms > select #4/A:28 5 atoms, 4 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select #4/A:27@C,O 2 atoms, 1 bond, 1 residue, 1 model selected > show sel atoms > select #4/A:27@C#2.1:38@N 5 atoms, 5 residues, 2 models selected Exactly two atoms must be selected! > select #4/A:27@C#2.1/A:38@N 2 atoms, 2 residues, 2 models selected > distance #4/A:27@C #2.1/A:38@N Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/A GLY 27 C and LH2_Sphaeroides.pdb 1 #2.1/A THR 38 N: 1.023Å > align #4/A:27 toAtoms #2.1/A:37 matchAtomNames true move atoms Pairing dropped 1 atoms and 3 reference atoms RMSD between 4 atom pairs is 0.258 angstroms > align #4/A:27@CA,C,O toAtoms #2.1/A:37 matchAtomNames true move atoms Pairing dropped 0 atoms and 4 reference atoms RMSD between 3 atom pairs is 0.014 angstroms > ~distance #4/E:1@N #2.1/K:49@C > ~distance #4/C:1@N #4/E:28@C > select up 12 atoms, 10 bonds, 2 residues, 2 models selected > select #4/C:28@C#4/E:1@N 2 atoms, 2 residues, 1 model selected > distance #4/C:28@C #4/E:1@N Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/C GLY 28 C and /E GLY 1 N: 14.583Å > select #4/D:1@N#4/E:28@C 2 atoms, 2 residues, 1 model selected > distance #4/D:1@N #4/E:28@C Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/D GLY 1 N and /E GLY 28 C: 15.336Å > ~distance #4/D:28@C #2.1/K:48@N > select #2.1/K:48 7 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #2.1/K:48 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #2.1/K:49 14 atoms, 15 bonds, 1 residue, 1 model selected > select #2.1/K:50 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #2.1/K:50-55 13 atoms, 12 bonds, 2 residues, 1 model selected > show sel atoms > select #2.1/K:50-59 13 atoms, 12 bonds, 2 residues, 1 model selected > show sel atoms > select #2.1/K:52 Nothing selected > select #2.1/K:48-49 21 atoms, 23 bonds, 2 residues, 1 model selected > show sel atoms > select #2.1/K:47-49 28 atoms, 30 bonds, 1 pseudobond, 3 residues, 2 models selected > ~distance #4/D:1@N #4/E:28@C > ~distance #4/C:28@C #4/E:1@N > select #2.1/B:38 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2.1/B:39 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2.1/B:38 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2.1/B:38@N/A:45@C 2 atoms, 2 residues, 1 model selected > select #2.1/B:39@N/A:45@C 2 atoms, 2 residues, 1 model selected > distance #2.1/A:45@C #2.1/B:39@N Distance between LH2_Sphaeroides.pdb 1 #2.1/A TYR 45 C and /B THR 39 N: 7.111Å > ~distance #2.1/A:45@C #2.1/B:39@N > hide #!1 models > show #!1 models > hide #!2 models > select #4/B:1@N#4/D:28@C 2 atoms, 2 residues, 1 model selected > distance #4/B:1@N #4/D:28@C Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/B GLY 1 N and /D GLY 28 C: 13.085Å > select #4/D:1@N#4/C:28@C 2 atoms, 2 residues, 1 model selected > select #4/D:1@N#4/E:28@C 2 atoms, 2 residues, 1 model selected > distance #4/D:1@N #4/E:28@C Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/D GLY 1 N and /E GLY 28 C: 15.336Å > select #4/E:1@N#4/C:28@C 2 atoms, 2 residues, 1 model selected > distance #4/C:28@C #4/E:1@N Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/C GLY 28 C and /E GLY 1 N: 14.583Å > show #!2 models > select #2.1/K@OXT#4/B:1@N 2 atoms, 2 residues, 2 models selected > distance #4/B:1@N #2.1/K:51@OXT Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/B GLY 1 N and LH2_Sphaeroides.pdb 1 #2.1/K GLY 51 OXT: 13.347Å > ~distance #4/B:1@N #4/D:28@C > select #2.1/K:48@N#4/D:28@C 2 atoms, 2 residues, 2 models selected > distance #4/D:28@C #2.1/K:48@N Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/D GLY 28 C and LH2_Sphaeroides.pdb 1 #2.1/K PRO 48 N: 3.877Å > save ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB design p_ap_p_p_ap refine > and connect.cxs"" > combine #2.1#4 Name combine 5HB Expected a keyword > combine #2.1#4 Remapping chain ID 'A' in CCCP LH2 5HB p_ap_p_p_ap.pdb #4 to 'F' Remapping chain ID 'B' in CCCP LH2 5HB p_ap_p_p_ap.pdb #4 to 'G' > hide #!4 models > hide #!2 models > select #3/B 590 atoms, 593 bonds, 47 pseudobonds, 67 residues, 4 models selected > show #!4 models > hide sel atoms > hide #!4 models > select #3/B/A:11-32 744 atoms, 750 bonds, 45 pseudobonds, 89 residues, 4 models selected > hide sel atoms > select #3/B/A:11-32/J 1207 atoms, 1212 bonds, 64 pseudobonds, 151 residues, 4 models selected > select #3/A:11-45 260 atoms, 268 bonds, 11 pseudobonds, 35 residues, 2 models selected > show sel atoms > style sel stick Changed 260 atom styles > select #3/A:11-45/K:20-51 500 atoms, 514 bonds, 42 pseudobonds, 67 residues, 3 models selected > show sel atoms > style sel stick Changed 500 atom styles > select #3/A:11-45/K:20-51/J:20-47 706 atoms, 723 bonds, 38 pseudobonds, 95 residues, 3 models selected > show sel atoms > style sel stick Changed 706 atom styles > select #3/C/D/F/ Expected an objects specifier or a keyword > select #3/C/D/F 429 atoms, 428 bonds, 80 pseudobonds, 83 residues, 2 models selected > hide sel cartoons > hide sel atoms > delete atoms sel > delete bonds sel > show #!4 models > ui tool show ""Change Chain IDs"" > select #3/C/D/F Nothing selected > select #3/A 609 atoms, 608 bonds, 24 pseudobonds, 71 residues, 3 models selected > select #3/A/B 1199 atoms, 1201 bonds, 46 pseudobonds, 138 residues, 3 models selected > select #3/A 609 atoms, 608 bonds, 24 pseudobonds, 71 residues, 3 models selected > ui tool show ""Change Chain IDs"" > changechains sel C Chain IDs of 71 residues changed > select #3/J 463 atoms, 462 bonds, 17 pseudobonds, 62 residues, 3 models selected > changechains sel A Chain IDs of 62 residues changed > select #3/D Nothing selected > select #3/B 590 atoms, 593 bonds, 20 pseudobonds, 67 residues, 3 models selected > show sel cartoons > hide sel cartoons > hide #!4 models > show #!4 models > hide #!4 models > show #!2 models > hide #!2 models > select #3/B 590 atoms, 593 bonds, 20 pseudobonds, 67 residues, 3 models selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > select #3/B Nothing selected > show #!4 models > hide #!4 models > select #3/E 140 atoms, 139 bonds, 27 pseudobonds, 28 residues, 2 models selected > changechains sel B Chain IDs of 28 residues changed > show #!4 models > select #3/F Nothing selected > select #3/E Nothing selected > select #3/C 609 atoms, 608 bonds, 24 pseudobonds, 71 residues, 3 models selected > changechains sel E Chain IDs of 71 residues changed > select #3/K 467 atoms, 462 bonds, 16 pseudobonds, 66 residues, 3 models selected > changechains sel C Chain IDs of 66 residues changed > hide #!4 models > select #3/G 142 atoms, 141 bonds, 27 pseudobonds, 28 residues, 2 models selected > select #3/D Nothing selected > select #3/G 142 atoms, 141 bonds, 27 pseudobonds, 28 residues, 2 models selected > changechains sel D Chain IDs of 28 residues changed > select #3/A-E 1821 atoms, 1812 bonds, 151 pseudobonds, 255 residues, 5 models selected > save ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs"" > select #3 &~/A-E Nothing selected > select #3/A-E 1821 atoms, 1812 bonds, 151 pseudobonds, 255 residues, 5 models selected > select #3/A/C/D 1072 atoms, 1065 bonds, 60 pseudobonds, 156 residues, 4 models selected > select #3/A:20-47/C:20-51/E:11-45 706 atoms, 723 bonds, 18 pseudobonds, 95 residues, 2 models selected > hide sel atoms > select #3/A:20-47/C:20-51,101/E:11-45,101 838 atoms, 863 bonds, 60 pseudobonds, 97 residues, 4 models selected > hide sel atoms > show sel atoms > ~distance #4/A:27@C #2.1/A:38@N > ~distance #4/B:1@N #2.1/B:40@C > ~distance #4/A:1@N #4/B:28@C > ~distance #4/B:1@N #2.1/K:51@OXT > ~distance #4/D:28@C #2.1/K:48@N > ~distance #4/D:1@N #4/E:28@C > ~distance #4/C:28@C #4/E:1@N > select #3/A:20-47/C:20-51,101/E:11-45,101/B/D 1120 atoms, 1143 bonds, 114 pseudobonds, 153 residues, 5 models selected > show sel atoms > select #3 &~:BCL&~protein 197 atoms, 146 bonds, 51 residues, 1 model selected > show sel atoms > delete atoms sel > delete bonds sel > select #3:BCL 264 atoms, 280 bonds, 16 pseudobonds, 4 residues, 2 models selected > show sel atoms > select #3/A:BCL 66 atoms, 70 bonds, 4 pseudobonds, 1 residue, 2 models selected > hide sel atoms > show sel atoms > select #3/A:BCL/E:BCL 198 atoms, 210 bonds, 12 pseudobonds, 3 residues, 2 models selected > select #3/A:101/E:102 132 atoms, 140 bonds, 8 pseudobonds, 2 residues, 2 models selected > hide sel atoms > show sel atoms > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > save ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs"" ——— End of log from Tue Oct 17 13:50:43 2023 ——— opened ChimeraX session > select #3/E:1-19/A:1-19 263 atoms, 269 bonds, 34 residues, 1 model selected > select #3/C:1-19/A:1-19 226 atoms, 230 bonds, 30 residues, 1 model selected > show sel atoms > select #3/A:1 Nothing selected > select #3/A 353 atoms, 362 bonds, 4 pseudobonds, 47 residues, 2 models selected > select #3/A:47@C/B:1@N 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance #3/A:47@C #3/B:1@N Distance between combination #3/A THR 47 C and /B GLY 1 N: 16.032Å > select #3/B:28@C/C:16@N 2 atoms, 2 residues, 1 model selected > distance #3/C:16@N #3/B:28@C Distance between combination #3/C ALA 16 N and /B GLY 28 C: 10.723Å > select #3/C:1-15 85 atoms, 87 bonds, 11 residues, 1 model selected > hide sel atoms > select #3/C:51@C/D:1@N 2 atoms, 2 residues, 1 model selected > distance #3/C:51@C #3/D:1@N Distance between combination #3/C GLY 51 C and /D GLY 1 N: 13.421Å > select #3/E:1-10 83 atoms, 84 bonds, 10 residues, 1 model selected > show sel atoms > hide sel atoms > select #3/A:1-15 85 atoms, 87 bonds, 11 residues, 1 model selected > hide sel atoms > select #3/E:1-12 99 atoms, 101 bonds, 12 residues, 1 model selected > hide sel atoms > select #3/D:28@C/E:12@N 2 atoms, 2 residues, 1 model selected > distance #3/E:12@N #3/D:28@C Distance between combination #3/E PRO 12 N and /D GLY 28 C: 11.557Å > ~distance #3/E:12@N #3/D:28@C > select #3/D:28@C/E:13@N 2 atoms, 2 residues, 1 model selected > distance #3/E:13@N #3/D:28@C Distance between combination #3/E THR 13 N and /D GLY 28 C: 9.080Å > select #3/A:1-19 113 atoms, 115 bonds, 15 residues, 1 model selected > hide sel atoms > save ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs"" > select #3/A:1-19 113 atoms, 115 bonds, 15 residues, 1 model selected > delete atoms sel > delete bonds sel > color #!3 bychain > color #!3 byhetero > select #3/A 240 atoms, 246 bonds, 4 pseudobonds, 32 residues, 2 models selected > select #3/C:1-15 85 atoms, 87 bonds, 11 residues, 1 model selected > delete atoms sel > delete bonds sel > select #3/E:47-59 20 atoms, 19 bonds, 4 residues, 1 model selected > show sel atoms > hide sel atoms > select #3/E:1-12 99 atoms, 101 bonds, 12 residues, 1 model selected > show sel atoms > delete atoms sel > delete bonds sel > select #3/E:46-59 29 atoms, 28 bonds, 5 residues, 1 model selected > show sel atoms > delete atoms sel > delete bonds sel > select :BCL 1914 atoms, 2030 bonds, 116 pseudobonds, 29 residues, 6 models selected > select #3:BCL 132 atoms, 140 bonds, 8 pseudobonds, 2 residues, 2 models selected > select #3:BCL@C[123456789],C[12][0123456789] 40 atoms, 38 bonds, 2 residues, 1 model selected > hide sel atoms > delete atoms sel > delete bonds sel > save ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs"" > select #3 1126 atoms, 1151 bonds, 65 pseudobonds, 159 residues, 5 models selected > show sel atoms > select #3/A:48-51 34 atoms, 36 bonds, 4 residues, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs"" ——— End of log from Tue Oct 17 14:26:21 2023 ——— opened ChimeraX session > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > close #2 > close #4 > combine #1 close true modelID 4 Expected a keyword > help help:user > combine #1 close true modelId 4 No structures specified > combine #1 No structures specified > combine #3 > select #2/B 140 atoms, 139 bonds, 28 residues, 1 model selected > select #2/B:1@N/A:47@C 2 atoms, 2 residues, 1 model selected > ui tool show Distances > ui tool show ""Build Structure"" > build join peptide sel length 16 omega 180 phi -120 move N Atoms must be in different models > split #2 Split copy of combination (#2) into 5 models Chain information for copy of combination A #2.1 --- Chain | Description A | No description available Chain information for copy of combination B #2.2 --- Chain | Description B | No description available Chain information for copy of combination C #2.3 --- Chain | Description C | No description available Chain information for copy of combination D #2.4 --- Chain | Description D | No description available Chain information for copy of combination E #2.5 --- Chain | Description E | No description available > select #2/B:1@N/A:47@C 2 atoms, 2 residues, 2 models selected > build join peptide sel length 16 omega 180 phi -120 move N C-terminal carbon not bonded to exactly one carbon > select #2/A:47@TMP 1 atom, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select #2/B:1@N/A:47@C 2 atoms, 2 residues, 2 models selected > build join peptide sel length 16 omega 180 phi -120 move N > align #2.1:48-75 toAtoms #3/B matchAtomNames true move atoms RMSD between 140 atom pairs is 0.000 angstroms > hide #!3 models > select #2/C:16@N/A:75@C 2 atoms, 2 residues, 2 models selected > save ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs"" ——— End of log from Tue Oct 17 18:18:24 2023 ——— opened ChimeraX session > select #2.3:BCL 46 atoms, 50 bonds, 4 pseudobonds, 1 residue, 2 models selected > ui tool show ""Renumber Residues"" > renumber #2.3/C:101 start 201 relative false 1 residues renumbered > select #2.5:BCL 46 atoms, 50 bonds, 4 pseudobonds, 1 residue, 2 models selected > renumber #2.5/E:101 start 202 relative false 1 residues renumbered > select #2/C:16@N/A:75@C 2 atoms, 2 residues, 2 models selected > ui tool show ""Build Structure"" > build join peptide sel length 4 omega 180 phi -120 move N > show #!3 models > hide #!3 models > show #!3 models > align #2.1:91-126,201 toAtoms #3/C matchAtomNames true move atoms RMSD between 314 atom pairs is 0.000 angstroms > hide #!3 models > save ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs"" > select #2@OXT 1 atom, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select #2/D:1@N/A:126@C 2 atoms, 2 residues, 2 models selected > build join peptide sel length 4 omega 180 phi -120 move N > show #!3 models > align #2.1:127-154 toAtoms #3/D matchAtomNames true move atoms RMSD between 142 atom pairs is 0.000 angstroms > hide #!3 models > select #2/E:13@N/A:154@C 2 atoms, 2 residues, 2 models selected > build join peptide sel length 4 omega 180 phi -120 move N > select #2/A:167-202 336 atoms, 351 bonds, 20 pseudobonds, 35 residues, 3 models selected > select #2/A:167-199,202 290 atoms, 301 bonds, 16 pseudobonds, 34 residues, 3 models selected > select #2/A:167-200,202 290 atoms, 301 bonds, 16 pseudobonds, 34 residues, 3 models selected > select #2/A:167-201,202 336 atoms, 351 bonds, 20 pseudobonds, 35 residues, 3 models selected > select #2/A:167-199,202 290 atoms, 301 bonds, 16 pseudobonds, 34 residues, 3 models selected > align #2.1:167-199,202 toAtoms #3/E matchAtomNames true move atoms RMSD between 290 atom pairs is 0.000 angstroms > save ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs"" > align #2.1:47@C:48@N Missing required ""to_atoms"" argument > select #2.1:47@C:48@N 2 atoms, 1 bond, 2 residues, 1 model selected > ~bond sel > select #2.1:75@C:91@N 2 atoms, 1 bond, 2 residues, 1 model selected > ~bond sel > select #2.1:126@C:127@N 2 atoms, 1 bond, 2 residues, 1 model selected > ~bond sel > select #2.1:154@C:167@N 2 atoms, 1 bond, 2 residues, 1 model selected > ~bond sel > save ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs"" ——— End of log from Tue Oct 17 18:44:05 2023 ——— opened ChimeraX session > open ""/Users/drornoy/Desktop/ChimeraX cleaner/clean.py"" executed clean.py > save ""/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs"" OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache: 16 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 12.5.1 (21G83) Kernel Version: Darwin 21.6.0 Time since boot: 20 days 5:27 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 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: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 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: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 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: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 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: 1.1.1 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: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 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: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 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: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 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: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 File attachment: LH2 5HB for design.cxs }}} [attachment:""LH2 5HB for design.cxs""] " defect assigned normal Sessions Tom Goddard all ChimeraX