Opened 5 years ago

Closed 5 years ago

#4152 closed enhancement (fixed)

alt loc starting values

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
If I try to create new altlocs for a set of atoms by:

{{{
for a in selected_atoms(session)
a.set_alt_loc('A', True)
}}}

... then all the coordinates for the new altlocs (or the master coordinates if there were no previous altlocs) are set to (0,0,0). I think it would be more sensible if the new ones inherited the existing coordinates as a starting point.

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> alias st isolde step $*

> alias aw isolde add water $*

> alias awsf isolde add water sim false

UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open working.pdb

Summary of feedback from opening working.pdb  
---  
warnings | Ignored bad PDB record found on line 243  
LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN  
  
Ignored bad PDB record found on line 244  
LINKR TYR L 184 LEU L 186 gap  
  
Ignored bad PDB record found on line 245  
LINKR VAL L 210 GLU L 212 gap  
  
Ignored bad PDB record found on line 246  
LINKR PRO A 140 GLY A 148 gap  
  
working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
R | No description available  
  
Non-standard residues in working.pdb #1  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  

> isolde start

> set selectionWidth 4

working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/H | No description available  
1.2/L | No description available  
1.2/R | No description available  
  
Non-standard residues in working.pdb #1.2  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  
Done loading forcefield  
Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  

> view /B:92

Loading residue template for GOL from internal database  
Loading residue template for SO4 from internal database  
Updating bulk solvent parameters...  

> select clear

> select clear

Updating bulk solvent parameters...  

> view /A:59

> select clear

Updating bulk solvent parameters...  

> view /A:213

> select clear

Updating bulk solvent parameters...  

> view /A:179

> view /H:179

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select clear

> select clear

Updating bulk solvent parameters...  

> save working.pdb #1

> close #1

Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_18  
Deleting (LIVE) MDFF potential  

> open working_refine_001.pdb

Chain information for working_refine_001.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
R | No description available  
  
Chain information for working_refine_001.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/H | No description available  
1.2/L | No description available  
1.2/R | No description available  
  
Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  

> open
> /run/media/tic20/storage/structure_dump/consultancy/vir/2021_01_90qnB2/working.pdb

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/consultancy/vir/2021_01_90qnB2/working.pdb  
---  
warnings | Ignored bad PDB record found on line 243  
LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN  
  
Ignored bad PDB record found on line 244  
LINKR TYR L 184 LEU L 186 gap  
  
Ignored bad PDB record found on line 245  
LINKR VAL L 210 GLU L 212 gap  
  
Ignored bad PDB record found on line 246  
LINKR PRO A 140 GLY A 148 gap  
  
working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
R | No description available  
  
Non-standard residues in working.pdb #2  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  

> close #2

> close #1

Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_18  
Deleting (LIVE) MDFF potential  

> open
> /run/media/tic20/storage/structure_dump/papers/2020_study_weekend/examples/3fyj_ref_3fhr/ref_to_isolde_rebuild/Refine_56/3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb
> format pdb

Chain information for 3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb #1  
---  
Chain | Description  
X | No description available  
  
Chain information for 3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb  
---  
Chain | Description  
1.2/X | No description available  
  

> close #1

> open working.pdb

Summary of feedback from opening working.pdb  
---  
warnings | Ignored bad PDB record found on line 243  
LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN  
  
Ignored bad PDB record found on line 244  
LINKR TYR L 184 LEU L 186 gap  
  
Ignored bad PDB record found on line 245  
LINKR VAL L 210 GLU L 212 gap  
  
Ignored bad PDB record found on line 246  
LINKR PRO A 140 GLY A 148 gap  
  
working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
R | No description available  
  
Non-standard residues in working.pdb #1  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  
working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/H | No description available  
1.2/L | No description available  
1.2/R | No description available  
  
Non-standard residues in working.pdb #1.2  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  

> view /R:449

> delete /R:616

Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  

> set bgColor white

Loading residue template for POL from internal database  

> select clear

Updating bulk solvent parameters...  

> open 6m0j

6m0j title:  
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
[more info...]  
  
Chain information for 6m0j #2  
---  
Chain | Description  
A | Angiotensin-converting enzyme 2  
E | Spike receptor binding domain  
  
Non-standard residues in 6m0j #2  
---  
CL — chloride ion  
NAG — N-acetyl-D-glucosamine  
ZN — zinc ion  
  

> matchmaker #2 to #1/R

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 working.pdb, chain R (#1.2) with 6m0j, chain E (#2), sequence
alignment score = 1012.9  
RMSD between 192 pruned atom pairs is 0.602 angstroms; (across all 194 pairs:
0.726)  
  

> show #2

> close #2

> view /R:604

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> select :HOH

1284 atoms, 856 bonds, 428 residues, 1 model selected  

> clipper isolate sel contextDistance 0

> clipper isolate sel contextDistance 0

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> select clear

Updating bulk solvent parameters...  

> select :HOH

1281 atoms, 854 bonds, 427 residues, 1 model selected  

> delete sel

> close #1

Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_18  
Deleting (LIVE) MDFF potential  

> open working.pdb

Summary of feedback from opening working.pdb  
---  
warnings | Ignored bad PDB record found on line 243  
LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN  
  
Ignored bad PDB record found on line 244  
LINKR TYR L 184 LEU L 186 gap  
  
Ignored bad PDB record found on line 245  
LINKR VAL L 210 GLU L 212 gap  
  
Ignored bad PDB record found on line 246  
LINKR PRO A 140 GLY A 148 gap  
  
working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
R | No description available  
  
Non-standard residues in working.pdb #1  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  
working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/H | No description available  
1.2/L | No description available  
1.2/R | No description available  
  
Non-standard residues in working.pdb #1.2  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  
Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  

> select up

6 atoms, 4 bonds, 2 residues, 1 model selected  

> delete sel

> select clear

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> select clear

> select #1

17592 atoms, 17354 bonds, 2 pseudobonds, 1532 residues, 30 models selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> select clear

Updating bulk solvent parameters...  

> view /R:449

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

> select clear

Updating bulk solvent parameters...  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> view /R:449

> awsf

> awsf

> awsf

> awsf

> awsf

> select clear

Updating bulk solvent parameters...  

> st first

> st

> st interp 2

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> aw

> isolde sim start sel

Updating bulk solvent parameters...  

> st

> st

> st

> st

> aw

> isolde sim start sel

> select clear

Updating bulk solvent parameters...  

> aw

> isolde sim start sel

Updating bulk solvent parameters...  

> st

> st

> st

> st

> st

> aw

> isolde sim start sel

> select clear

Updating bulk solvent parameters...  

> st

> aw

> isolde sim start sel

> select clear

Updating bulk solvent parameters...  

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> aw

> isolde sim start sel

Updating bulk solvent parameters...  

> awsf

> awsf

> awsf

> select clear

Updating bulk solvent parameters...  

> select up

9 atoms, 6 bonds, 3 residues, 1 model selected  

> delete sel

> st

> st

> st

> st

> st

> st

> aw

> isolde sim start sel

> select clear

Updating bulk solvent parameters...  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> alias al isolde add ligand $*

> alias so setattr sel atoms occupancy $*

> al SO4

> so 0.7

Assigning occupancy attribute to 5 items  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  
Updating bulk solvent parameters...  

> select up

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

> so 0.5

Assigning occupancy attribute to 5 items  

> st

> st

> st

> st

> st

> awsf

> awsf

Updating bulk solvent parameters...  

> st

> st

> st

> al GOL

> select clear

Updating bulk solvent parameters...  

> st

> aw

> isolde sim start sel

Updating bulk solvent parameters...  

> awsf

> awsf

Updating bulk solvent parameters...  

> select up

9 atoms, 6 bonds, 3 residues, 1 model selected  

> delete sel

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> al BMA

Deleted the following atoms from residue BMA R710: HO1, O1  

> show sel

> ui mousemode right "translate selected atoms"

> delete sel

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py", line
1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/menu/menu.py", line 58, in f  
module.run_script(session)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/menu/model_building/make_bond.py", line 22, in
run_script  
add_bond(*sel)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/struct_edit.py", line 225, in add_bond  
\+ all_residues[i1+1:i2] + all_residues[end_range+1:]  
TypeError: unsupported operand type(s) for +: 'Residues' and 'Residues'  
  
TypeError: unsupported operand type(s) for +: 'Residues' and 'Residues'  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/struct_edit.py", line 225, in add_bond  
\+ all_residues[i1+1:i2] + all_residues[end_range+1:]  
  
See log for complete Python traceback.  
  

> select clear

> select up

22 atoms, 22 bonds, 1 residue, 1 model selected  
Updating bulk solvent parameters...  

> al MAN

Deleted the following atoms from residue MAN R711: HO1, O1  

> show sel

> ui mousemode right "translate selected atoms"

> delete sel

> select clear

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

Updating bulk solvent parameters...  

> select up

22 atoms, 22 bonds, 1 residue, 1 model selected  

> delete sel

Updating bulk solvent parameters...  

> delete sel

> save working_2.pdb #1

> view /R:449

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select sel&sideonly

15 atoms, 15 bonds, 1 residue, 1 model selected  




OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         12G         36G        303M         13G         49G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Async: 0.1
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-Phenix: 0.1
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    graphviz: 0.14.1
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    objgraph: 3.4.1
    openvr: 1.12.501
    packaging: 20.4
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    Send2Trash: 1.5.0
    SEQCROW: 0.20
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    versioneer: 0.18
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (3)

in reply to:  1 ; comment:1 by Tristan Croll, 5 years ago 

Also, occupancies are filled with uninitialised values and B-factors are zero. Would be better if the new altlocs inherited all the properties of the parent, and even better if the occupancies were automatically divided in two (a pretty reasonable starting point in most cases).
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 21 January 2021 18:27
To: Tristan Croll <tic20@cam.ac.uk>
Subject: [ChimeraX] #4152: ChimeraX bug report submission

#4152: ChimeraX bug report submission
---------------------------+-----------------------------
 Reporter:  Tristan Croll  |                Type:  defect
   Status:  new            |            Priority:  normal
Component:  Unassigned     |          Blocked By:
 Blocking:                 |  Notify when closed:
---------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-
 centos-7.8.2003-Core
 ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
 Description
 If I try to create new altlocs for a set of atoms by:

 {{{
 for a in selected_atoms(session)
 a.set_alt_loc('A', True)
 }}}

 ... then all the coordinates for the new altlocs (or the master
 coordinates if there were no previous altlocs) are set to (0,0,0). I think
 it would be more sensible if the new ones inherited the existing
 coordinates as a starting point.

 Log:
 > alias preview_toolshed toolshed url https://cxtoolshed-
 > preview.rbvi.ucsf.edu; toolshed reload available

 > alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
 > toolshed reload available

 > alias st isolde step $*

 > alias aw isolde add water $*

 > alias awsf isolde add water sim false

 UCSF ChimeraX version: 1.1 (2020-09-09)
 © 2016-2020 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > open working.pdb

 Summary of feedback from opening working.pdb
 ---
 warnings | Ignored bad PDB record found on line 243
 LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN

 Ignored bad PDB record found on line 244
 LINKR TYR L 184 LEU L 186 gap

 Ignored bad PDB record found on line 245
 LINKR VAL L 210 GLU L 212 gap

 Ignored bad PDB record found on line 246
 LINKR PRO A 140 GLY A 148 gap

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb #1
 ---
 Chain | Description
 A | No description available
 B | No description available
 H | No description available
 L | No description available
 R | No description available

 Non-standard residues in working.pdb #1
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)


 > isolde start

 > set selectionWidth 4

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb
 ---
 Chain | Description
 1.2/A | No description available
 1.2/B | No description available
 1.2/H | No description available
 1.2/L | No description available
 1.2/R | No description available

 Non-standard residues in working.pdb #1.2
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)

 Done loading forcefield
 Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM
 Y
 Reflection data provided as intensities. Performing French & Wilson
 scaling to
 convert to amplitudes...

 > view /B:92

 Loading residue template for GOL from internal database
 Loading residue template for SO4 from internal database
 Updating bulk solvent parameters...

 > select clear

 > select clear

 Updating bulk solvent parameters...

 > view /A:59

 > select clear

 Updating bulk solvent parameters...

 > view /A:213

 > select clear

 Updating bulk solvent parameters...

 > view /A:179

 > view /H:179

 > ui tool show Shell

 /opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/IPython/core/history.py:226:
 UserWarning: IPython History requires SQLite, your history will not be
 saved
 warn("IPython History requires SQLite, your history will not be saved")

 > select clear

 > select clear

 Updating bulk solvent parameters...

 > save working.pdb #1

 > close #1

 Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)
 Deleting (LIVE) 2mFo-DFc
 Deleting (LIVE) mFo-DFc
 Deleting (LIVE) 2mFo-DFc_smooth_18
 Deleting (LIVE) MDFF potential

 > open working_refine_001.pdb

 Chain information for working_refine_001.pdb #1
 ---
 Chain | Description
 A | No description available
 B | No description available
 H | No description available
 L | No description available
 R | No description available

 Chain information for working_refine_001.pdb
 ---
 Chain | Description
 1.2/A | No description available
 1.2/B | No description available
 1.2/H | No description available
 1.2/L | No description available
 1.2/R | No description available

 Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM
 Y
 Reflection data provided as intensities. Performing French & Wilson
 scaling to
 convert to amplitudes...

 > open
 >
 /run/media/tic20/storage/structure_dump/consultancy/vir/2021_01_90qnB2/working.pdb

 Summary of feedback from opening
 /run/media/tic20/storage/structure_dump/consultancy/vir/2021_01_90qnB2/working.pdb
 ---
 warnings | Ignored bad PDB record found on line 243
 LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN

 Ignored bad PDB record found on line 244
 LINKR TYR L 184 LEU L 186 gap

 Ignored bad PDB record found on line 245
 LINKR VAL L 210 GLU L 212 gap

 Ignored bad PDB record found on line 246
 LINKR PRO A 140 GLY A 148 gap

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb #2
 ---
 Chain | Description
 A | No description available
 B | No description available
 H | No description available
 L | No description available
 R | No description available

 Non-standard residues in working.pdb #2
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)


 > close #2

 > close #1

 Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)
 Deleting (LIVE) 2mFo-DFc
 Deleting (LIVE) mFo-DFc
 Deleting (LIVE) 2mFo-DFc_smooth_18
 Deleting (LIVE) MDFF potential

 > open
 >
 /run/media/tic20/storage/structure_dump/papers/2020_study_weekend/examples/3fyj_ref_3fhr/ref_to_isolde_rebuild/Refine_56/3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb
 > format pdb

 Chain information for 3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb #1
 ---
 Chain | Description
 X | No description available

 Chain information for 3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb
 ---
 Chain | Description
 1.2/X | No description available


 > close #1

 > open working.pdb

 Summary of feedback from opening working.pdb
 ---
 warnings | Ignored bad PDB record found on line 243
 LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN

 Ignored bad PDB record found on line 244
 LINKR TYR L 184 LEU L 186 gap

 Ignored bad PDB record found on line 245
 LINKR VAL L 210 GLU L 212 gap

 Ignored bad PDB record found on line 246
 LINKR PRO A 140 GLY A 148 gap

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb #1
 ---
 Chain | Description
 A | No description available
 B | No description available
 H | No description available
 L | No description available
 R | No description available

 Non-standard residues in working.pdb #1
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb
 ---
 Chain | Description
 1.2/A | No description available
 1.2/B | No description available
 1.2/H | No description available
 1.2/L | No description available
 1.2/R | No description available

 Non-standard residues in working.pdb #1.2
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)


 > view /R:449

 > delete /R:616

 Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM
 Y
 Reflection data provided as intensities. Performing French & Wilson
 scaling to
 convert to amplitudes...

 > set bgColor white

 Loading residue template for POL from internal database

 > select clear

 Updating bulk solvent parameters...

 > open 6m0j

 6m0j title:
 Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with
 ACE2
 [more info...]

 Chain information for 6m0j #2
 ---
 Chain | Description
 A | Angiotensin-converting enzyme 2
 E | Spike receptor binding domain

 Non-standard residues in 6m0j #2
 ---
 CL — chloride ion
 NAG — N-acetyl-D-glucosamine
 ZN — zinc ion


 > matchmaker #2 to #1/R

 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 working.pdb, chain R (#1.2) with 6m0j, chain E (#2), sequence
 alignment score = 1012.9
 RMSD between 192 pruned atom pairs is 0.602 angstroms; (across all 194
 pairs:
 0.726)


 > show #2

 > close #2

 > view /R:604

 > select up

 3 atoms, 2 bonds, 1 residue, 1 model selected

 > delete sel

 > select :HOH

 1284 atoms, 856 bonds, 428 residues, 1 model selected

 > clipper isolate sel contextDistance 0

 > clipper isolate sel contextDistance 0

 > select up

 3 atoms, 2 bonds, 1 residue, 1 model selected

 > delete sel

 > select clear

 Updating bulk solvent parameters...

 > select :HOH

 1281 atoms, 854 bonds, 427 residues, 1 model selected

 > delete sel

 > close #1

 Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)
 Deleting (LIVE) 2mFo-DFc
 Deleting (LIVE) mFo-DFc
 Deleting (LIVE) 2mFo-DFc_smooth_18
 Deleting (LIVE) MDFF potential

 > open working.pdb

 Summary of feedback from opening working.pdb
 ---
 warnings | Ignored bad PDB record found on line 243
 LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN

 Ignored bad PDB record found on line 244
 LINKR TYR L 184 LEU L 186 gap

 Ignored bad PDB record found on line 245
 LINKR VAL L 210 GLU L 212 gap

 Ignored bad PDB record found on line 246
 LINKR PRO A 140 GLY A 148 gap

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb #1
 ---
 Chain | Description
 A | No description available
 B | No description available
 H | No description available
 L | No description available
 R | No description available

 Non-standard residues in working.pdb #1
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb
 ---
 Chain | Description
 1.2/A | No description available
 1.2/B | No description available
 1.2/H | No description available
 1.2/L | No description available
 1.2/R | No description available

 Non-standard residues in working.pdb #1.2
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)

 Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM
 Y
 Reflection data provided as intensities. Performing French & Wilson
 scaling to
 convert to amplitudes...

 > select up

 6 atoms, 4 bonds, 2 residues, 1 model selected

 > delete sel

 > select clear

 > select up

 3 atoms, 2 bonds, 1 residue, 1 model selected

 > delete sel

 > select clear

 > select #1

 17592 atoms, 17354 bonds, 2 pseudobonds, 1532 residues, 30 models selected
 Map is too large for fast cubic interpolation on the GPU! Switching to
 slower,
 more memory-efficient implementation.

 > select clear

 Updating bulk solvent parameters...

 > view /R:449

 > select up

 21 atoms, 21 bonds, 1 residue, 1 model selected

 > select clear

 > select clear

 Updating bulk solvent parameters...

 > select up

 3 atoms, 2 bonds, 1 residue, 1 model selected

 > delete sel

 > view /R:449

 > awsf

 > awsf

 > awsf

 > awsf

 > awsf

 > select clear

 Updating bulk solvent parameters...

 > st first

 > st

 > st interp 2

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > aw

 > isolde sim start sel

 Updating bulk solvent parameters...

 > st

 > st

 > st

 > st

 > aw

 > isolde sim start sel

 > select clear

 Updating bulk solvent parameters...

 > aw

 > isolde sim start sel

 Updating bulk solvent parameters...

 > st

 > st

 > st

 > st

 > st

 > aw

 > isolde sim start sel

 > select clear

 Updating bulk solvent parameters...

 > st

 > aw

 > isolde sim start sel

 > select clear

 Updating bulk solvent parameters...

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > aw

 > isolde sim start sel

 Updating bulk solvent parameters...

 > awsf

 > awsf

 > awsf

 > select clear

 Updating bulk solvent parameters...

 > select up

 9 atoms, 6 bonds, 3 residues, 1 model selected

 > delete sel

 > st

 > st

 > st

 > st

 > st

 > st

 > aw

 > isolde sim start sel

 > select clear

 Updating bulk solvent parameters...

 > select up

 3 atoms, 2 bonds, 1 residue, 1 model selected

 > delete sel

 > alias al isolde add ligand $*

 > alias so setattr sel atoms occupancy $*

 > al SO4

 > so 0.7

 Assigning occupancy attribute to 5 items

 > select up

 5 atoms, 4 bonds, 1 residue, 1 model selected
 Updating bulk solvent parameters...

 > select up

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

 > so 0.5

 Assigning occupancy attribute to 5 items

 > st

 > st

 > st

 > st

 > st

 > awsf

 > awsf

 Updating bulk solvent parameters...

 > st

 > st

 > st

 > al GOL

 > select clear

 Updating bulk solvent parameters...

 > st

 > aw

 > isolde sim start sel

 Updating bulk solvent parameters...

 > awsf

 > awsf

 Updating bulk solvent parameters...

 > select up

 9 atoms, 6 bonds, 3 residues, 1 model selected

 > delete sel

 > select up

 3 atoms, 2 bonds, 1 residue, 1 model selected

 > delete sel

 > al BMA

 Deleted the following atoms from residue BMA R710: HO1, O1

 > show sel

 > ui mousemode right "translate selected atoms"

 > delete sel

 Traceback (most recent call last):
 File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py",
 line
 1574, in <lambda>
 action.triggered.connect(lambda arg, cb = callback: cb())
 File "/home/tic20/.local/share/ChimeraX/1.1/site-
 packages/chimerax/isolde/menu/menu.py", line 58, in f
 module.run_script(session)
 File "/home/tic20/.local/share/ChimeraX/1.1/site-
 packages/chimerax/isolde/menu/model_building/make_bond.py", line 22, in
 run_script
 add_bond(*sel)
 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/chimerax/atomic/struct_edit.py", line 225, in add_bond
 \+ all_residues[i1+1:i2] + all_residues[end_range+1:]
 TypeError: unsupported operand type(s) for +: 'Residues' and 'Residues'

 TypeError: unsupported operand type(s) for +: 'Residues' and 'Residues'

 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/chimerax/atomic/struct_edit.py", line 225, in add_bond
 \+ all_residues[i1+1:i2] + all_residues[end_range+1:]

 See log for complete Python traceback.


 > select clear

 > select up

 22 atoms, 22 bonds, 1 residue, 1 model selected
 Updating bulk solvent parameters...

 > al MAN

 Deleted the following atoms from residue MAN R711: HO1, O1

 > show sel

 > ui mousemode right "translate selected atoms"

 > delete sel

 > select clear

 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
 bonded heavy atom.

 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
 bonded heavy atom.

 Updating bulk solvent parameters...

 > select up

 22 atoms, 22 bonds, 1 residue, 1 model selected

 > delete sel

 Updating bulk solvent parameters...

 > delete sel

 > save working_2.pdb #1

 > view /R:449

 > select up

 21 atoms, 21 bonds, 1 residue, 1 model selected

 > select sel&sideonly

 15 atoms, 15 bonds, 1 residue, 1 model selected




 OpenGL version: 3.3.0 NVIDIA 455.32.00
 OpenGL renderer: TITAN Xp/PCIe/SSE2
 OpenGL vendor: NVIDIA Corporation
 Manufacturer: Dell Inc.
 Model: Precision T5600
 OS: CentOS Linux 7 Core
 Architecture: 64bit ELF
 CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
 Cache Size: 20480 KB
 Memory:
                       total        used        free      shared
 buff/cache   available
         Mem:            62G         12G         36G        303M
 13G         49G
         Swap:          4.9G          0B        4.9G

 Graphics:
         03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102
 [TITAN Xp] [10de:1b02] (rev a1)
         Subsystem: NVIDIA Corporation Device [10de:11df]
         Kernel driver in use: nvidia
 PyQt version: 5.12.3
 Compiled Qt version: 5.12.4
 Runtime Qt version: 5.12.9
 Installed Packages:
     alabaster: 0.7.12
     appdirs: 1.4.4
     Babel: 2.8.0
     backcall: 0.2.0
     blockdiag: 2.0.1
     certifi: 2020.6.20
     chardet: 3.0.4
     ChimeraX-AddH: 2.1.1
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.1
     ChimeraX-Arrays: 1.0
     ChimeraX-Async: 0.1
     ChimeraX-Atomic: 1.6.1
     ChimeraX-AtomSearch: 2.0
     ChimeraX-AxesPlanes: 2.0
     ChimeraX-BasicActions: 1.1
     ChimeraX-BILD: 1.0
     ChimeraX-BlastProtein: 1.0.1
     ChimeraX-BondRot: 2.0
     ChimeraX-BugReporter: 1.0
     ChimeraX-BuildStructure: 2.0
     ChimeraX-Bumps: 1.0
     ChimeraX-BundleBuilder: 1.0
     ChimeraX-ButtonPanel: 1.0
     ChimeraX-CageBuilder: 1.0
     ChimeraX-CellPack: 1.0
     ChimeraX-Centroids: 1.1
     ChimeraX-ChemGroup: 2.0
     ChimeraX-Clashes: 2.0
     ChimeraX-Clipper: 0.15.0
     ChimeraX-ColorActions: 1.0
     ChimeraX-ColorGlobe: 1.0
     ChimeraX-CommandLine: 1.1.3
     ChimeraX-ConnectStructure: 2.0
     ChimeraX-Contacts: 1.0
     ChimeraX-Core: 1.1
     ChimeraX-CoreFormats: 1.0
     ChimeraX-coulombic: 1.0.1
     ChimeraX-Crosslinks: 1.0
     ChimeraX-Crystal: 1.0
     ChimeraX-DataFormats: 1.0
     ChimeraX-Dicom: 1.0
     ChimeraX-DistMonitor: 1.1
     ChimeraX-DistUI: 1.0
     ChimeraX-Dssp: 2.0
     ChimeraX-EMDB-SFF: 1.0
     ChimeraX-ExperimentalCommands: 1.0
     ChimeraX-FileHistory: 1.0
     ChimeraX-FunctionKey: 1.0
     ChimeraX-Geometry: 1.1
     ChimeraX-gltf: 1.0
     ChimeraX-Graphics: 1.0
     ChimeraX-Hbonds: 2.0
     ChimeraX-Help: 1.0
     ChimeraX-HKCage: 1.3
     ChimeraX-IHM: 1.0
     ChimeraX-ImageFormats: 1.0
     ChimeraX-IMOD: 1.0
     ChimeraX-IO: 1.0
     ChimeraX-ISOLDE: 1.1.0
     ChimeraX-Label: 1.0
     ChimeraX-LinuxSupport: 1.0
     ChimeraX-ListInfo: 1.0
     ChimeraX-Log: 1.1.1
     ChimeraX-LookingGlass: 1.1
     ChimeraX-Map: 1.0.1
     ChimeraX-MapData: 2.0
     ChimeraX-MapEraser: 1.0
     ChimeraX-MapFilter: 2.0
     ChimeraX-MapFit: 2.0
     ChimeraX-MapSeries: 2.0
     ChimeraX-Markers: 1.0
     ChimeraX-Mask: 1.0
     ChimeraX-MatchMaker: 1.1
     ChimeraX-MDcrds: 2.0
     ChimeraX-MedicalToolbar: 1.0.1
     ChimeraX-Meeting: 1.0
     ChimeraX-MLP: 1.0
     ChimeraX-mmCIF: 2.2
     ChimeraX-MMTF: 2.0
     ChimeraX-Modeller: 1.0
     ChimeraX-ModelPanel: 1.0
     ChimeraX-ModelSeries: 1.0
     ChimeraX-Mol2: 2.0
     ChimeraX-Morph: 1.0
     ChimeraX-MouseModes: 1.0
     ChimeraX-Movie: 1.0
     ChimeraX-Neuron: 1.0
     ChimeraX-Nucleotides: 2.0
     ChimeraX-OpenCommand: 1.2.1
     ChimeraX-PDB: 2.1
     ChimeraX-PDBBio: 1.0
     ChimeraX-Phenix: 0.1
     ChimeraX-PickBlobs: 1.0
     ChimeraX-Positions: 1.0
     ChimeraX-PresetMgr: 1.0
     ChimeraX-PubChem: 2.0
     ChimeraX-Read-Pbonds: 1.0
     ChimeraX-Registration: 1.1
     ChimeraX-RemoteControl: 1.0
     ChimeraX-ResidueFit: 1.0
     ChimeraX-RestServer: 1.0
     ChimeraX-RNALayout: 1.0
     ChimeraX-RotamerLibMgr: 2.0
     ChimeraX-RotamerLibsDunbrack: 2.0
     ChimeraX-RotamerLibsDynameomics: 2.0
     ChimeraX-RotamerLibsRichardson: 2.0
     ChimeraX-SaveCommand: 1.2
     ChimeraX-SchemeMgr: 1.0
     ChimeraX-SDF: 2.0
     ChimeraX-Segger: 1.0
     ChimeraX-Segment: 1.0
     ChimeraX-SeqView: 2.2
     ChimeraX-Shape: 1.0.1
     ChimeraX-Shell: 1.0
     ChimeraX-Shortcuts: 1.0
     ChimeraX-ShowAttr: 1.0
     ChimeraX-ShowSequences: 1.0
     ChimeraX-SideView: 1.0
     ChimeraX-Smiles: 2.0
     ChimeraX-SmoothLines: 1.0
     ChimeraX-SpaceNavigator: 1.0
     ChimeraX-StdCommands: 1.0.4
     ChimeraX-STL: 1.0
     ChimeraX-Storm: 1.0
     ChimeraX-Struts: 1.0
     ChimeraX-Surface: 1.0
     ChimeraX-SwapAA: 2.0
     ChimeraX-SwapRes: 2.0
     ChimeraX-TapeMeasure: 1.0
     ChimeraX-Test: 1.0
     ChimeraX-Toolbar: 1.0
     ChimeraX-ToolshedUtils: 1.0
     ChimeraX-Tug: 1.0
     ChimeraX-UI: 1.2.3
     ChimeraX-uniprot: 2.0
     ChimeraX-ViewDockX: 1.0
     ChimeraX-Vive: 1.1
     ChimeraX-VolumeMenu: 1.0
     ChimeraX-VTK: 1.0
     ChimeraX-WavefrontOBJ: 1.0
     ChimeraX-WebCam: 1.0
     ChimeraX-WebServices: 1.0
     ChimeraX-Zone: 1.0
     colorama: 0.4.3
     comtypes: 1.1.7
     cxservices: 1.0
     cycler: 0.10.0
     Cython: 0.29.20
     decorator: 4.4.2
     distlib: 0.3.1
     distro: 1.5.0
     docutils: 0.16
     filelock: 3.0.12
     funcparserlib: 0.3.6
     grako: 3.16.5
     graphviz: 0.14.1
     h5py: 2.10.0
     html2text: 2020.1.16
     idna: 2.10
     ihm: 0.16
     imagecodecs: 2020.5.30
     imagecodecs-lite: 2020.1.31
     imagesize: 1.2.0
     ipykernel: 5.3.0
     ipython: 7.15.0
     ipython-genutils: 0.2.0
     jedi: 0.17.2
     Jinja2: 2.11.2
     jupyter-client: 6.1.3
     jupyter-core: 4.6.3
     kiwisolver: 1.2.0
     line-profiler: 2.1.2
     lxml: 4.5.1
     MarkupSafe: 1.1.1
     matplotlib: 3.2.1
     msgpack: 1.0.0
     netifaces: 0.10.9
     networkx: 2.4
     numexpr: 2.7.1
     numpy: 1.18.5
     numpydoc: 1.0.0
     objgraph: 3.4.1
     openvr: 1.12.501
     packaging: 20.4
     ParmEd: 3.2.0
     parso: 0.7.1
     pexpect: 4.8.0
     pickleshare: 0.7.5
     Pillow: 7.1.2
     pip: 20.2.2
     pkginfo: 1.5.0.1
     prompt-toolkit: 3.0.7
     psutil: 5.7.0
     ptyprocess: 0.6.0
     pycollada: 0.7.1
     pydicom: 2.0.0
     Pygments: 2.6.1
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
     pyparsing: 2.4.7
     PyQt5-commercial: 5.12.3
     PyQt5-sip: 4.19.19
     PyQtWebEngine-commercial: 5.12.1
     python-dateutil: 2.8.1
     pytz: 2020.1
     pyzmq: 19.0.2
     qtconsole: 4.7.4
     QtPy: 1.9.0
     RandomWords: 0.3.0
     requests: 2.24.0
     scipy: 1.4.1
     Send2Trash: 1.5.0
     SEQCROW: 0.20
     setuptools: 49.4.0
     sfftk-rw: 0.6.6.dev0
     six: 1.15.0
     snowballstemmer: 2.0.0
     sortedcontainers: 2.2.2
     Sphinx: 3.1.1
     sphinxcontrib-applehelp: 1.0.2
     sphinxcontrib-blockdiag: 2.0.0
     sphinxcontrib-devhelp: 1.0.2
     sphinxcontrib-htmlhelp: 1.0.3
     sphinxcontrib-jsmath: 1.0.1
     sphinxcontrib-qthelp: 1.0.3
     sphinxcontrib-serializinghtml: 1.1.4
     suds-jurko: 0.6
     tables: 3.6.1
     tifffile: 2020.6.3
     tinyarray: 1.2.2
     tornado: 6.0.4
     traitlets: 5.0.4
     urllib3: 1.25.10
     versioneer: 0.18
     wcwidth: 0.2.5
     webcolors: 1.11.1
     wheel: 0.34.2

 }}}

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4152>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
Version 0, edited 5 years ago by Tristan Croll (next)

comment:2 by Eric Pettersen, 5 years ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → alt loc starting values
Type: defect → enhancement

comment:3 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed

I assigned the bfactor, coordinate, and serial_number to their previous values if there were any. I set occupancy to zero. I didn't use the suggested occupancy behavior because it would lead to unexpected behavior in this very common scenario:

create an alt loc

set bfactor, coordinate, and occupancy

create next alt loc

set bfactor, coordinate, and occupancy

meanwhile creating the second alt loc changed the occupancy of the first one.

--Eric

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