Opened 4 years ago

Closed 4 years ago

#5718 closed defect (fixed)

Bond-rotation mouse mode: excess atoms

Reported by: Tristan Croll Owned by: pett
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.3rc202111182158 (2021-11-18 21:58:36 UTC)
Description
Got stuck in an interesting little loop here when I used the bond rotation mousemode on a residue which happened to have a rotamer preview displayed in ISOLDE. Problem is that the rotamer preview is actually a trivial subclass of `AtomicStructure` (i.e. unmodified, subclassed only so it can easily be distinguished programmatically from a true `AtomicStructure`). Did it that way because it made a bunch of things much, much easier... but in its brief life it lives as a submodel of ISOLDE's rotamer restraints manager, which in turn is a submodel of a submodel of the AtomicStructure. Upshot is that the torsion command ends up finding 8 atoms where it expects 4, and things get stuck because almost every attempt to change the selection triggers that callback. Could be avoided by making the torsion command more specific (i.e. #!1.2 instead of #1.2)... or I could try reworking my code.

Log:
UCSF ChimeraX version: 1.3rc202111182158 (2021-11-18)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:\Users\tristan\structure_dump\genentech\6vmj\working.cxs format
> session

Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 1,1,1, pixel 0.706,0.706,0.704,
shown at level 0.234, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 1,1,1, pixel 0.706,0.706,0.704,
shown at level -0.113,0.113, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_28 as #1.1.1.4, grid size 1,1,1, pixel
0.706,0.706,0.704, shown at level 0.585, step 1, values float32  
Opened (LIVE) MDFF potential as #1.1.1.8, grid size 1,1,1, pixel
0.706,0.706,0.704, shown at level 0.295, step 1, values float32  
Restoring stepper: 6vmj  
Log from Wed Dec 1 21:20:19 2021

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3rc202111182158 (2021-11-18)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6vbn structureFactors true

Summary of feedback from opening 6vbn fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_anom_difference, pdbx_anom_difference_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 6vbn from
http://files.rcsb.org/download/6vbn.cif  
Fetching CCD QVY from http://ligand-expo.rcsb.org/reports/Q/QVY/QVY.cif  
Fetching compressed 6vbn structure factors from
http://files.rcsb.org/download/6vbn-sf.cif  
Resolution: 3.180033012291658  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 28,28,24, pixel
0.981,0.993,1.02, shown at level 0.124, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 28,28,24, pixel 0.981,0.993,1.02,
shown at level -0.0724,0.0724, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_35 as #1.1.1.4, grid size 28,28,24, pixel
0.981,0.993,1.02, shown at level 0.277, step 1, values float32  
6vbn title:  
Crystal Structure of hTDO2 bound to inhibitor GNE1 [more info...]  
  
Chain information for 6vbn  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C 1.2/D | Tryptophan 2,3-dioxygenase | T23O_HUMAN  
  
Non-standard residues in 6vbn #1.2  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
QVY — 1,5-anhydro-2,3-dideoxy-3-[(5S)-5H-imidazo[5,1-a]isoindol-5-yl]-D-threo-
pentitol  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 128 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 28,28,24, pixel
0.981,0.993,1.02, shown at level 0.14, step 1, values float32  
Done loading forcefield  

> addh template true

Summary of feedback from adding hydrogens to 6vbn #1.2  
---  
notes | Termini for 6vbn (#1.2) chain A determined from SEQRES records  
Termini for 6vbn (#1.2) chain B determined from SEQRES records  
Termini for 6vbn (#1.2) chain C determined from SEQRES records  
Termini for 6vbn (#1.2) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A LEU 40, /B LEU 40, /C
LEU 40, /D LEU 40  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A PRO 383, /B ASN 382, /C
THR 384, /D ASN 382  
1460 hydrogen bonds  
Adding 'H' to /A LEU 40  
Adding 'H' to /B LEU 40  
Adding 'H' to /C LEU 40  
Adding 'H' to /D LEU 40  
/A PRO 383 is not terminus, removing H atom from 'C'  
/B ASN 382 is not terminus, removing H atom from 'C'  
/C THR 384 is not terminus, removing H atom from 'C'  
/D ASN 382 is not terminus, removing H atom from 'C'  
11773 hydrogens added  
  
Deleted the following atoms from residue HEM D401: HAD2, HMB2, HBD1, HBD2,
HMB3, HMA2, FE, HMB1, HAA1, HMD1, HMA1, HBC2, HMD2, HMD3, HMA3, HAA2, HMC3,
HAD1, HBB1, HBA1, HBB2, HMC2, HBA2, HMC1, HBC1  
Deleted the following atoms from residue HEM C401: HBA2, HMB1, HMA2, HMB3,
HAA1, HMC2, HMD1, HAA2, HBB1, HBA1, HAD2, HBD1, HAD1, HBD2, HMC1, FE, HBC2,
HMD2, HMA3, HMC3, HMB2, HBB2, HMA1, HMD3, HBC1  
Deleted the following atoms from residue HEM B401: HMA2, HMB2, HBB1, HBC1,
HMC3, HBC2, HBB2, HMC1, HMA3, HAA2, HBD1, HMD1, HAA1, HBD2, HBA1, HMA1, HMD3,
HBA2, HMB1, FE, HAD1, HMD2, HMB3, HAD2, HMC2  
Deleted the following atoms from residue HEM A401: HBD1, HMB3, HBD2, HBC2,
HMA3, HMB1, HMD1, HMC2, HBB1, HMA1, HBB2, HMD2, HAD1, HMC3, FE, HMA2, HAA2,
HBC1, HBA1, HMB2, HAD2, HMD3, HBA2, HMC1, HAA1  

> select up

35 atoms, 38 bonds, 1 residue, 1 model selected  

> isolde parameterise sel

Parameterisation of QVY failed with the following message:  

'Ring' object has no attribute '_c_pointer_ref'  

> isolde parameterise sel

Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\tristan\AppData\Local\Temp\tmpeqosuek8\ante.in.mol2 -fi mol2 -o
C:\Users\tristan\AppData\Local\Temp\tmpeqosuek8\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(QVY) ``  
(QVY) `Welcome to antechamber 20.0: molecular input file processor.`  
(QVY) ``  
(QVY) `Info: Finished reading file
(C:\Users\tristan\AppData\Local\Temp\tmpeqosuek8\ante.in.mol2); atoms read
(35), bonds read (38).`  
(QVY) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(QVY) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(QVY) `bash.exe: warning: could not find /tmp, please create!`  
(QVY) ``  
(QVY) ``  
(QVY) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(QVY) `bash.exe: warning: could not find /tmp, please create!`  
(QVY) `Info: Total number of electrons: 136; net charge: 0`  
(QVY) ``  
(QVY) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(QVY) `bash.exe: warning: could not find /tmp, please create!`  
(QVY) ``  
(QVY) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(QVY) `bash.exe: warning: could not find /tmp, please create!`  
(QVY) ``  
(QVY) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(QVY) `bash.exe: warning: could not find /tmp, please create!`  
(QVY) ``  
Charges for residue QVY determined  
OpenMM ffXML file QVY written to the current working directory.  
New template added to forcefield as USER_QVY. This ligand should now work in
all remaining simulations for this session. To use in future sessions, load
the ffXML file with ISOLDE's Load Residue MD Definition(s) button.  

> select up

73 atoms, 80 bonds, 1 residue, 1 model selected  

> show sel

> select #1

23658 atoms, 23928 bonds, 1419 residues, 24 models selected  
ISOLDE: started sim  

> select clear

ISOLDE: paused sim  
ISOLDE: resumed sim  

> select clear

ISOLDE: paused sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 18 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select clear

Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> delete :HOH

ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> alphafold match #1

Fetching compressed AlphaFold P48775 from
https://alphafold.ebi.ac.uk/files/AF-P48775-F1-model_v1.cif  
1 AlphaFold model found using UniProt identifier: P48775 (chains A,B,C,D)  
AlphaFold chains matching 6vbn  
---  
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id  
A | T23O_HUMAN | P48775 | 1.15 | 371 | 344 | 100  
B | T23O_HUMAN | P48775 | 1.37 | 371 | 343 | 100  
C | T23O_HUMAN | P48775 | 1.14 | 371 | 345 | 100  
D | T23O_HUMAN | P48775 | 1.01 | 371 | 343 | 100  
  
Opened 4 AlphaFold models  

> isolde restrain distances #1/A templateAtoms #2/A adjustForConfidence true

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 87 residues in
model #2.1 to IUPAC-IUB standards.  
Fetching compressed Alphafold P48775 PAE from
https://alphafold.ebi.ac.uk/files/AF-P48775-F1-predicted_aligned_error_v1.json  
RMSD between 341 pruned atom pairs is 0.926 angstroms; (across all 344 pairs:
1.146)  

> isolde restrain distances #1/B templateAtoms #2/B adjustForConfidence true

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 87 residues in
model #2.2 to IUPAC-IUB standards.  
RMSD between 339 pruned atom pairs is 1.112 angstroms; (across all 343 pairs:
1.352)  
RMSD between 3 pruned atom pairs is 2.049 angstroms; (across all 4 pairs:
3.999)  

> isolde restrain distances #1/C templateAtoms #2/C adjustForConfidence true

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 87 residues in
model #2.3 to IUPAC-IUB standards.  
RMSD between 342 pruned atom pairs is 0.957 angstroms; (across all 345 pairs:
1.139)  

> isolde restrain distances #1/D templateAtoms #2/D adjustForConfidence true

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 87 residues in
model #2.4 to IUPAC-IUB standards.  
RMSD between 340 pruned atom pairs is 0.795 angstroms; (across all 343 pairs:
1.006)  

> isolde restrain torsions #1/A templateResidues #2/A adjustForConfidence true

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> isolde restrain torsions #1/B templateResidues #2/A adjustForConfidence true

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> isolde restrain torsions #1/C templateResidues #2/A adjustForConfidence true

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> isolde restrain torsions #1/D templateResidues #2/A adjustForConfidence true

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> isolde adjust distances #1 displayThreshold 0.5

> hide #!2 models

> select #1

23550 atoms, 23856 bonds, 1383 residues, 30 models selected  
ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]ISOLDE: paused sim  

> show #!2 models

> hide #!2 models

> show #!2 models

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> rd

ISOLDE: resumed sim  
ISOLDE: paused sim  

> ra

ISOLDE: resumed sim  
ISOLDE: paused sim  

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> ra

ISOLDE: resumed sim  

> ra

> select clear

> ra

[Repeated 2 time(s)]Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> close #1.3#1-2#1.1-2

Deleting Crystallographic maps (6vbn-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_35  
Deleting (LIVE) MDFF potential  

> open 6vmj structureFactors true overSampling 2

Summary of feedback from opening 6vmj fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_HL_A_iso, pdbx_HL_B_iso, pdbx_HL_C_iso, pdbx_HL_D_iso,  
phase_calc, fom  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 6vmj from
http://files.rcsb.org/download/6vmj.cif  
Fetching compressed 6vmj structure factors from
http://files.rcsb.org/download/6vmj-sf.cif  
Resolution: 2.9500451440648137  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,36,36, pixel
0.706,0.706,0.704, shown at level 0.234, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,36,36, pixel
0.706,0.706,0.704, shown at level -0.1,0.1, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_28 as #1.1.1.4, grid size 36,36,36, pixel
0.706,0.706,0.704, shown at level 0.585, step 1, values float32  
Opened (STATIC) F_calc_au, phase_calc as #1.1.1.5, grid size 36,36,36, pixel
0.706,0.706,0.704, shown at level -0.433,0.433, step 1, values float32  
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.6, grid size 36,36,36,
pixel 0.706,0.706,0.704, shown at level -0.202,0.202, step 1, values float32  
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.7, grid size 36,36,36, pixel
0.706,0.706,0.704, shown at level -0.475,0.475, step 1, values float32  
6vmj title:  
Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12
[more info...]  
  
Chain information for 6vmj  
---  
Chain | Description | UniProt  
1.2/A 1.2/E 1.2/I 1.2/L | Fab20D12 Light Chain |  
1.2/B 1.2/F 1.2/J 1.2/M | Fab20D12 heavy chain |  
1.2/W 1.2/X 1.2/Y 1.2/Z | Complement factor D | CFAD_HUMAN  
  
Non-standard residues in 6vmj #1.2  
---  
CIT — citric acid  
  
6vmj mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 1050, in _update_model_list  
self._change_selected_model(model=current_model)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2521, in _change_selected_model  
m.delete_alt_locs()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1590, in delete_alt_locs  
f = c_function('structure_delete_alt_locs', args =
(ctypes.c_void_p,))(self._c_pointer)  
OSError: exception: access violation reading 0x0000000000000014  
  
Error processing trigger "add models":  
OSError: exception: access violation reading 0x0000000000000014  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1590, in delete_alt_locs  
f = c_function('structure_delete_alt_locs', args =
(ctypes.c_void_p,))(self._c_pointer)  
  
See log for complete Python traceback.  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 141 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.8, grid size 36,36,36, pixel
0.706,0.706,0.704, shown at level 0.295, step 1, values float32  
Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to 6vmj #1.2  
---  
notes | Termini for 6vmj (#1.2) chain A determined from SEQRES records  
Termini for 6vmj (#1.2) chain B determined from SEQRES records  
Termini for 6vmj (#1.2) chain E determined from SEQRES records  
Termini for 6vmj (#1.2) chain F determined from SEQRES records  
Termini for 6vmj (#1.2) chain I determined from SEQRES records  
7 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ASP 1, /B GLU 1, /E ASP
1, /F GLU 1, /I ASP 1, /J GLU 1, /L ASP 1, /M GLU 1, /W ILE 16, /X ILE 16, /Y
ILE 16, /Z ILE 16  
Chain-initial residues that are not actual N termini: /B GLY 133, /F GLY 133,
/J GLY 133, /M GLY 133  
Chain-final residues that are actual C termini: /W ALA 243, /X ALA 243, /Y ALA
243, /Z ALA 243  
Chain-final residues that are not actual C termini: /A GLU 213, /B SER 128, /B
PRO 213, /E GLU 213, /F SER 128, /F PRO 213, /I GLU 213, /J SER 128, /J PRO
213, /L GLU 213, /M SER 128, /M SER 215  
2771 hydrogen bonds  
Adding 'H' to /B GLY 133  
Adding 'H' to /F GLY 133  
Adding 'H' to /J GLY 133  
Adding 'H' to /M GLY 133  
/A GLU 213 is not terminus, removing H atom from 'C'  
/B PRO 213 is not terminus, removing H atom from 'C'  
/E GLU 213 is not terminus, removing H atom from 'C'  
/F PRO 213 is not terminus, removing H atom from 'C'  
/I GLU 213 is not terminus, removing H atom from 'C'  
3 messages similar to the above omitted  
19608 hydrogens added  
  
Loading residue template for CIT from internal database  

> select #1

39536 atoms, 39843 bonds, 4 pseudobonds, 2767 residues, 37 models selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 48 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  

> set bgColor white

Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> alphafold match /X

Fetching compressed AlphaFold P00746 from
https://alphafold.ebi.ac.uk/files/AF-P00746-F1-model_v1.cif  
1 AlphaFold model found using UniProt identifier: P00746 (chain X)  
AlphaFold chains matching 6vmj  
---  
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id  
X | CFAD_HUMAN | P00746 | 0.45 | 228 | 228 | 100  
  
Opened 1 AlphaFold model  

> show #2

> hide #!2 models

ISOLDE: started sim  

> select clear

> cbb

41248 atoms, 2995 residues, atom bfactor range 0 to 172  

> cbc

Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> show #!2 models

> hide #!2 models

> aw

> isolde sim start sel

ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> aw

> isolde sim start sel

ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select clear

Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> ui tool show Shell

> delete sel

ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select #1

39539 atoms, 39845 bonds, 4 pseudobonds, 2768 residues, 43 models selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
ISOLDE: started sim  

> select clear

Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 19 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> cbb

41251 atoms, 2996 residues, atom bfactor range 0 to 172  

> cbc

> close #1.1.1.5-7

ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> aw

> isolde sim start sel

ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> ht ND

Set protonation of HIS #1.2/Y:171 to ND  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

ISOLDE: started sim  

> usage isolde sim

isolde sim cmd [atoms] [discardTo discardTo]  
— Start, stop or pause an interactive simulation  
cmd: one of checkpoint, pause, revert, start, or stop  
discardTo: one of checkpoint or start  

> isolde sim stop

Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select clear

Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  

> select clear

Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> cd C:/Users/tristan/structure_dump/genentech/6vmj

Current working directory is: C:\Users\tristan\structure_dump\genentech\6vmj  

> save working.cxs

Taking snapshot of stepper: 6vmj  

——— End of log from Wed Dec 1 21:20:19 2021 ———

opened ChimeraX session  

> select up

322 atoms, 329 bonds, 20 residues, 1 model selected  

> isolde sim start #1

> set selectionWidth 4

Loading residue template for CIT from internal database  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
ISOLDE: started sim  
Done loading forcefield  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 16 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start #1

Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 14 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start #1

Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 10 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

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

> ui mousemode right "bond rotation"

> torsion #1.2/F:35@CD1,CG,CB,CA 86.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 86.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 86.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 86.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 86.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> ui mousemode right select

> torsion #1.2/F:35@CD1,CG,CB,CA 86.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 86.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 86.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 26.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 26.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 77.28

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 77.28

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 82.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 82.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 82.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 82.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 79.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 79.78

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 85.28

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 85.28

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> torsion #1.2/F:35@CD1,CG,CB,CA 85.28

Must specify exactly 4 atoms for 'torsion' command; you specified 8  

> ui tool show Shell

> select #1.2.4.1.1

21 atoms, 21 bonds, 1 residue, 1 model selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 1086, in _selection_changed  
self._enable_rebuild_residue_frame(r)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 1688, in
_enable_rebuild_residue_frame  
chain_id, resnum, resname = (res.chain_id, res.number, res.name)  
File "atomic_cpp\cymol.pyx", line 1013, in
chimerax.atomic.cymol.CyResidue.chain_id.__get__  
RuntimeError: Residue already deleted  
  
Error processing trigger "selection changed":  
RuntimeError: Residue already deleted  
  
File "atomic_cpp\cymol.pyx", line 1013, in
chimerax.atomic.cymol.CyResidue.chain_id.__get__  
  
See log for complete Python traceback.  
  

> torsion #1.2/F:35@CD1,CG,CB,CA 85.28

> select clear

[Repeated 1 time(s)]

> ui mousemode right "bond rotation"

> torsion #1.2/F:35@CD1,CG,CB,CA 87.28




OpenGL version: 3.3.0 NVIDIA 471.11
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    -himerax-clipper: 0.17.0
    -himerax-isolde: 1.3.dev33
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.2
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3rc202111182158
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3.dev33
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.22
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    python-igraph: 0.9.7
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    texttable: 1.6.4
    tifffile: 2021.4.8
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    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
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    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (6)

comment:1 by pett, 4 years ago

Cc: pett added
Component: Unassigned → Structure Editing
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Bond-rotation mouse mode: excess atoms

It seems that on mouse up, the mouse mode not only logs the command equivalent, it actually runs what it believes is the equivalent 'torsion' command. So either the code needs to generate an actual equivalent (perhaps as per your suggested change) or it needs to use chimerax.core.commands.log_equivalent_command to only log the command. Combining both would be optimal, since there is no need to actually execute the command.

comment:2 by pett, 4 years ago

Depending on what is decided, this may need to be reassigned to me -- to get res.string() and atom.string() to look down the model hierarchy to see if there are any Structures that are submodels of the structure in question.

comment:3 by Tom Goddard, 4 years ago

Cc: Tom Goddard added; pett removed
Owner: changed from Tom Goddard to pett

It is not reasonable to log a torsion command that doesn't actually work and just not run it. The logged command should of course work, and not rely on the user hopefully having removed the rotamer clones first.

The bond rotation mouse mode uses residue.string(style = 'command') and atom.string(style = 'command') and I guess those methods are intended to provide specifier strings that uniquely specify the residue and atom. But you have done something so bizarre by making other atomic models that are submodels of the atomic model and with identical chain identifiers, residue numbers and atom names, that it is no surprise those methods fail to give a correct specifier. I see why you handled your rotamers that way. Eric can decide if that is just too big a hack to accommodate. Does "torsion #!1.2/F:35@CD1,CG,CB,CA 85.28" with the exclamation mark work? I never tried. Making atomic models that are submodels of other atomic models seems likely to produce errors on almost every ChimeraX analysis command that takes an atom specifier.

comment:4 by pett, 4 years ago

The Rotamers tool does the same thing, so I'm pretty sure we need to get this to work. I'll fix up the string() routines.

in reply to:  5 ; comment:5 by pett, 4 years ago 

Well, not necessarily the same number / chain ID though.  Still...

comment:6 by pett, 4 years ago

Resolution: → fixed
Status: assigned → closed

The generated atom spec now uses '#!' if there are structure submodels. Only in 1.4 branch.

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