Opened 2 years ago

Closed 2 years ago

#10362 closed defect (fixed)

Mouse modes goes bananas

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.7rc202311140124 (2023-11-14 01:24:52 UTC)
Description
Merged a ligand generated from SMILES (which is loaded with a chain ID of "?") into ISOLDE's working model. Used the "bond rotation" mouse mode on it, leading to the error "Must specify exactly 4 atoms for 'torsion' command; you specified 8" being spammed to the log (it does actually still rotate the bond, though). That's not the fun part, though: it's left the session completely borked, with *every* mouse button (with or without modifier keys) all going to rotation of the bond I originally clicked, even though that mouse mode is no longer assigned to anything (see below - note that the modes with the generic "mode name" are Clipper modes... I'll see about fixing that):

for b in session.ui.mouse_modes.bindings:
    print(f'{b.modifiers}-{b.button}: {b.mode.name}')
    
[]-middle: translate
[]-pause: identify object
['control']-left: select
['control', 'shift']-left: select add
['control', 'alt']-left: select subtract
['shift']-right: zoom
[]-wheel: zoom
['shift']-wheel: mode name
['control']-middle: mode name
['control']-wheel: mode name
['alt']-wheel: mode name
[]-left: rotate
[]-right: isolde tug atom 

Log:
> 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: 1.7rc202311140124 (2023-11-14)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7pe8

Summary of feedback from opening 7pe8 fetched from pdb  
---  
note | Fetching compressed mmCIF 7pe8 from
http://files.rcsb.org/download/7pe8.cif  
  
7pe8 title:  
cryo-EM structure of DEPTOR bound to human mTOR complex 2, focussed on one
protomer [more info...]  
  
Chain information for 7pe8 #1  
---  
Chain | Description | UniProt  
A | Serine/threonine-protein kinase mTOR | MTOR_HUMAN 1-2549  
C | Target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326  
E | Rapamycin-insensitive companion of mTOR | RICTR_HUMAN 1-1708  
G | Target of rapamycin complex 2 subunit MAPKAP1 | SIN1_HUMAN 1-522  
I | DEP domain-containing mTOR-interacting protein | DPTOR_HUMAN 1-409  
  
Non-standard residues in 7pe8 #1  
---  
ACE — acetyl group  
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)  
ZN — zinc ion  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 203 residues in model #1 to IUPAC-IUB
standards.  
7pe8 title:  
cryo-EM structure of DEPTOR bound to human mTOR complex 2, focussed on one
protomer [more info...]  
  
Chain information for 7pe8  
---  
Chain | Description | UniProt  
1.2/A | Serine/threonine-protein kinase mTOR | MTOR_HUMAN 1-2549  
1.2/C | Target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326  
1.2/E | Rapamycin-insensitive companion of mTOR | RICTR_HUMAN 1-1708  
1.2/G | Target of rapamycin complex 2 subunit MAPKAP1 | SIN1_HUMAN 1-522  
1.2/I | DEP domain-containing mTOR-interacting protein | DPTOR_HUMAN 1-409  
  
Non-standard residues in 7pe8 #1.2  
---  
ACE — acetyl group  
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)  
ZN — zinc ion  
  

> log metadata #1.2

Metadata for 7pe8 #1.2  
---  
Title | cryo-EM structure of DEPTOR bound to human mTOR complex 2, focussed on
one protomer  
Citations | Walchli, M., Berneiser, K., Mangia, F., Imseng, S., Craigie, L.M.,
Stuttfeld, E., Hall, M.N., Maier, T. (2021). Regulation of human mTOR
complexes by DEPTOR. Elife, 10. PMID: 34519268. DOI: 10.7554/eLife.70871  
(2018). ISOLDE: a physically realistic environment for model building into
low-resolution electron density maps. Acta Cryst. D, 74(6), 519-530. PMID:
29872003. DOI: 10.1107/S2059798318002425  
Non-standard residues | ACE — acetyl group  
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)  
ZN — zinc ion  
Gene source | Homo sapiens (human)  
CryoEM Map | EMDB 13348 — open map  
Experimental method | Electron microscopy  
Resolution | 3.20Å  
  
> open 13348 fromDatabase emdb

Summary of feedback from opening 13348 fetched from emdb  
---  
notes | Fetching compressed map 13348 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-13348/map/emd_13348.map.gz  
Fetching map header 13348 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-13348/header/emd-13348.xml  
open kw {'initial_surface_level': 0.185}  
  
Opened emdb 13348 as #2, grid size 480,480,480, pixel 1.06, shown at level
0.185, step 2, values float32, fit PDB 7pe8  

> clipper associate #2 toModel #1

Opened emdb 13348 as #1.1.1.1, grid size 480,480,480, pixel 1.06, shown at
step 1, values float32  

> select :IHP

36 atoms, 36 bonds, 1 residue, 1 model selected  

> view sel

> rainbow /C

> open 4jsn

Summary of feedback from opening 4jsn fetched from pdb  
---  
note | Fetching compressed mmCIF 4jsn from
http://files.rcsb.org/download/4jsn.cif  
  
4jsn title:  
structure of mTORdeltaN-mLST8 complex [more info...]  
  
Chain information for 4jsn #2  
---  
Chain | Description | UniProt  
A B | Serine/threonine-protein kinase mTOR | MTOR_HUMAN 1376-2549  
C D | Target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326  
  
4jsn mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> matchmaker #2 to #1/C

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 7pe8, chain C (#1.2) with 4jsn, chain D (#2), sequence alignment
score = 1636.7  
RMSD between 293 pruned atom pairs is 0.880 angstroms; (across all 317 pairs:
1.609)  
  

> close

> alphafold fetch Q8N2K0

Chain information for AlphaFold Q8N2K0 #1  
---  
Chain | Description | UniProt  
A | Lysophosphatidylserine lipase ABHD12 | ABD12_HUMAN 1-398  
  
Color AlphaFold Q8N2K0 by residue attribute pLDDT_score  

> show

> color byhetero

> select :75-95

161 atoms, 165 bonds, 21 residues, 1 model selected  

> style sel sphere

Changed 161 atom styles  

> style sel ball

Changed 161 atom styles  

> ui tool show "2D Builder"

Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

> isolde select #1

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 67 residues in model #1 to IUPAC-IUB
standards.  
Chain information for AlphaFold Q8N2K0  
---  
Chain | Description | UniProt  
1.2/A | Lysophosphatidylserine lipase ABHD12 | ABD12_HUMAN 1-398  
  
Color AlphaFold Q8N2K0 by residue attribute pLDDT_score  
ISOLDE: attempting to load PAE matrix for model #1.2 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.  

> alphafold pae #1.2 uniprotId Q8N2K0 plot false

Fetching compressed AlphaFold PAE Q8N2K0 from
https://alphafold.ebi.ac.uk/files/AF-Q8N2K0-F1-predicted_aligned_error_v4.json  
s1:
MRKRTEPVALEHERCAAAGSSSSGSAAAALDADCRLKQNLRLTGPAAAEPRCAADAGMKRALGRRKGVWLRLRKILFCVLGLYIAIPFLIKLCPGIQAKLIFLNFVRVPYFIDLKKPQDQGLNHTCNYYLQPEEDVTIGVWHTVPAVWWKNAQGKDQMWYEDALASSHPIILYLHGNAGTRGGDHRVELYKVLSSLGYHVVTFDYRGWGDSVGTPSERGMTYDALHVFDWIKARSGDNPVYIWGHSLGTGVATNLVRRLCERETPPDALILESPFTNIREEAKSHPFSVIYRYFPGFDWFFLDPITSSGIKFANDENVKHISCPLLILHAEDDPVVPFQLGRKLYSIAAPARSFRDFKVQFVPFHSDLGYRHKYIYKSPELPRILREFLGKSEPEHQH  
s2:
MRKRTEPVALEHERCAAAGSSSSGSAAAALDADCRLKQNLRLTGPAAAEPRCAADAGMKRALGRRKGVWLRLRKILFCVLGLYIAIPFLIKLCPGIQAKLIFLNFVRVPYFIDLKKPQDQGLNHTCNYYLQPEEDVTIGVWHTVPAVWWKNAQGKDQMWYEDALASSHPIILYLHGNAGTRGGDHRVELYKVLSSLGYHVVTFDYRGWGDSVGTPSERGMTYDALHVFDWIKARSGDNPVYIWGHSLGTGVATNLVRRLCERETPPDALILESPFTNIREEAKSHPFSVIYRYFPGFDWFFLDPITSSGIKFANDENVKHISCPLLILHAEDDPVVPFQLGRKLYSIAAPARSFRDFKVQFVPFHSDLGYRHKYIYKSPELPRILREFLGKSEPEHQH  

> isolde restrain distances "#1.2/A" templateAtoms "#1.2/A" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/A templateResidues #1.2/A adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> select :75-95

161 atoms, 165 bonds, 21 residues, 1 model selected  

> style sel ball

Changed 161 atom styles  

> clipper isolate #1

> select #2

56 atoms, 59 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

ISOLDE: merge models  
Merging models #2 into #1.2.  

> hide #2 models

> select up

56 atoms, 59 bonds, 1 residue, 1 model selected  

> isolde parameterise sel

UNK: number of electrons (286) + formal charge (+1) is odd; cannot compute
charges for radical species using AM1-BCC method  

> show sel

> select up

57 atoms, 60 bonds, 1 residue, 1 model selected  

> isolde parameterise sel netCharge 1

Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TRISTA~1\AppData\Local\Temp\tmpg9pexs8x\ante.in.mol2 -fi mol2 -o
C:\Users\TRISTA~1\AppData\Local\Temp\tmpg9pexs8x\ante.out.mol2 -fo mol2 -c bcc
-nc 1 -j 5 -s 2 -dr n  
(UNK) ``  
(UNK) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNK) ``  
(UNK) `Info: Finished reading file
(C:\Users\TRISTA~1\AppData\Local\Temp\tmpg9pexs8x\ante.in.mol2); atoms read
(57), bonds read (60).`  
(UNK) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNK) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) `Info: Total number of electrons: 286; net charge: 1`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) `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`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
(UNK) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(UNK) `bash.exe: warning: could not find /tmp, please create!`  
(UNK) ``  
Charges for residue UNK determined  
OpenMM ffXML file UNK written to the current working directory.  
New template added to forcefield as USER_UNK. 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.  

> addh protein

Summary of feedback from adding hydrogens to AlphaFold Q8N2K0 #1.2  
---  
notes | Termini for AlphaFold Q8N2K0 (#1.2) chain A determined from SEQRES
records  
Chain-initial residues that are actual N termini: AlphaFold Q8N2K0 #1.2/A MET
1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: AlphaFold Q8N2K0 #1.2/A HIS
398  
Chain-final residues that are not actual C termini:  
353 hydrogen bonds  
3154 hydrogens added  
  

> select up

57 atoms, 60 bonds, 1 residue, 1 model selected  

> select zone sel 8 extend true

Selected 719 atoms  

> graphics silhouettes false

> isolde sim start #2/a
> #1.2/A:86-87,89-91,96-110,173,175-180,183-187,208,245-248,278,281-288,290-291,297,300-302,305,334-337,371-374,376/a

ISOLDE: started sim  

> select clear

> isolde sim pause

> select up

57 atoms, 60 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> isolde sim resume

> ui mousemode right "isolde tug atom"

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select up

57 atoms, 60 bonds, 1 residue, 1 model selected  

> color :UNL orange

> color byhetero

> color :UNK orange

> color byhetero

> open C1CN(CCN1CCCN2C(=O)N3C=CC=CC3=N2)C4=CC(=CC=C4)Cl fromDatabase smiles

Translated SMILES to 3D structure via NCI web service (SMILES:
C1CN(CCN1CCCN2C(=O)N3C=CC=CC3=N2)C4=CC(=CC=C4)Cl)  

> setattr #3 res name TRZ

Assigning name attribute to 1 item  

> select #3

48 atoms, 51 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> isolde ignore :UNK

ISOLDE: currently ignoring 1 residues in model 1.2  
ISOLDE: currently ignoring 1 residues in model 2  

> hide :UNK

ISOLDE: merge models  
Merging models #3 into #1.2.  

> hide #3 models

> select up

48 atoms, 51 bonds, 1 residue, 1 model selected  

> show sel

> select up

49 atoms, 52 bonds, 1 residue, 1 model selected  

> isolde parameterise sel

Loading residue template for TRZ from internal database  
Residue name TRZ already corresponds to template MC_TRZ in the amber14
forcefield. If you wish to replace that template, re-run this command with
override=True  

> isolde parameterise sel override true

Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TRISTA~1\AppData\Local\Temp\tmphr7vs6lu\ante.in.mol2 -fi mol2 -o
C:\Users\TRISTA~1\AppData\Local\Temp\tmphr7vs6lu\ante.out.mol2 -fo mol2 -c bcc
-nc 1 -j 5 -s 2 -dr n  
(TRZ) ``  
(TRZ) `Welcome to antechamber 20.0: molecular input file processor.`  
(TRZ) ``  
(TRZ) `Info: Finished reading file
(C:\Users\TRISTA~1\AppData\Local\Temp\tmphr7vs6lu\ante.in.mol2); atoms read
(49), bonds read (52).`  
(TRZ) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(TRZ) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(TRZ) `bash.exe: warning: could not find /tmp, please create!`  
(TRZ) ``  
(TRZ) ``  
(TRZ) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(TRZ) `bash.exe: warning: could not find /tmp, please create!`  
(TRZ) `Info: Total number of electrons: 196; net charge: 1`  
(TRZ) ``  
(TRZ) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(TRZ) `bash.exe: warning: could not find /tmp, please create!`  
(TRZ) ``  
(TRZ) `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`  
(TRZ) `bash.exe: warning: could not find /tmp, please create!`  
(TRZ) ``  
(TRZ) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(TRZ) `bash.exe: warning: could not find /tmp, please create!`  
(TRZ) ``  
Charges for residue TRZ determined  
OpenMM ffXML file TRZ written to the current working directory.  
New template added to forcefield as USER_TRZ. 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 zone sel 8 extend true

Selected 854 atoms, 1 surfaces  

> isolde sim start #2/a
> #1.2/*/A:90,96-103,105,108,173-187,189-190,202,204-205,208,220,243-251,272-275,277-288,297,301-302,305,310,312,329,333-337,340,372-373
> #3/*

ISOLDE: started sim  

> select clear

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

[Repeated 1 time(s)]

> select up

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

> rd

> show :UNK

> isolde sim pause

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select up

49 atoms, 52 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> delete sel

> select up

49 atoms, 52 bonds, 1 residue, 1 model selected  

> isolde parameterise sel override true

Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TRISTA~1\AppData\Local\Temp\tmpw4pcdxzi\ante.in.mol2 -fi mol2 -o
C:\Users\TRISTA~1\AppData\Local\Temp\tmpw4pcdxzi\ante.out.mol2 -fo mol2 -c bcc
-nc 1 -j 5 -s 2 -dr n  
(TRZ) ``  
(TRZ) `Welcome to antechamber 20.0: molecular input file processor.`  
(TRZ) ``  
(TRZ) `Info: Finished reading file
(C:\Users\TRISTA~1\AppData\Local\Temp\tmpw4pcdxzi\ante.in.mol2); atoms read
(49), bonds read (52).`  
(TRZ) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(TRZ) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(TRZ) `bash.exe: warning: could not find /tmp, please create!`  
(TRZ) ``  
(TRZ) ``  
(TRZ) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(TRZ) `bash.exe: warning: could not find /tmp, please create!`  
(TRZ) `Info: Total number of electrons: 196; net charge: 1`  
(TRZ) ``  
(TRZ) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(TRZ) `bash.exe: warning: could not find /tmp, please create!`  
(TRZ) ``  
(TRZ) `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`  
(TRZ) `bash.exe: warning: could not find /tmp, please create!`  
(TRZ) ``  
(TRZ) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(TRZ) `bash.exe: warning: could not find /tmp, please create!`  
(TRZ) ``  
Charges for residue TRZ determined  
OpenMM ffXML file TRZ written to the current working directory.  
New template added to forcefield as USER_TRZ. 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.  

> ui mousemode right "bond rotation"

> torsion #1.2/?:1@N3,C7,C6,C5 38.00

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

> torsion #1.2/?:1@N3,C7,C6,C5 38.00

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

> torsion #1.2/?:1@N3,C7,C6,C5 64.00

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

> torsion #1.2/?:1@N3,C7,C6,C5 64.00

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

> torsion #1.2/?:1@N3,C7,C6,C5 62.00

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

> torsion #1.2/?:1@N3,C7,C6,C5 62.00

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

> torsion #1.2/?:1@N3,C7,C6,C5 15.50

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

> torsion #1.2/?:1@N3,C7,C6,C5 15.50

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

> torsion #1.2/?:1@N3,C7,C6,C5 20.50

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

> torsion #1.2/?:1@N3,C7,C6,C5 20.50

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

> torsion #1.2/?:1@N3,C7,C6,C5 43.00

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

> ui mousemode right "bond rotation"

> torsion #1.2/?:1@N3,C7,C6,C5 43.00

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

> torsion #1.2/?:1@N3,C7,C6,C5 43.00

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

> select zone sel 5 extend true

Selected 349 atoms  

> isolde sim start #2/a
> #1.2/*/A:100-101,103,176-178,185-186,245-247,278,281-282,285,287,335,372-373
> #3/*

ISOLDE: started sim  

> torsion #1.2/?:1@N3,C7,C6,C5 43.00

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

> torsion #1.2/?:1@N3,C7,C6,C5 43.00

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

> torsion #1.2/?:1@N3,C7,C6,C5 69.62

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

> torsion #1.2/?:1@N3,C7,C6,C5 70.91

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

> torsion #1.2/?:1@N3,C7,C6,C5 64.88

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

> torsion #1.2/?:1@N3,C7,C6,C5 54.49

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

> torsion #1.2/?:1@N3,C7,C6,C5 65.97

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

> torsion #1.2/?:1@N3,C7,C6,C5 89.13

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

> ui mousemode right "isolde tug atom"

> torsion #1.2/?:1@N3,C7,C6,C5 69.21

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

> torsion #1.2/?:1@N3,C7,C6,C5 71.48

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

> torsion #1.2/?:1@N3,C7,C6,C5 71.32

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

> torsion #1.2/?:1@N3,C7,C6,C5 69.85

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

> ui mousemode right "isolde tug residue"

> ui mousemode right "isolde tug atom"

> torsion #1.2/?:1@N3,C7,C6,C5 72.07

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

> torsion #1.2/?:1@N3,C7,C6,C5 74.27

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

> torsion #1.2/?:1@N3,C7,C6,C5 72.97

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

> torsion #1.2/?:1@N3,C7,C6,C5 71.95

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

> isolde sim pause

> torsion #1.2/?:1@N3,C7,C6,C5 71.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 95.96

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

> ui mousemode right "isolde tug residue"

> ui mousemode right "isolde tug atom"

> torsion #1.2/?:1@N3,C7,C6,C5 95.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 105.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 105.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 82.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 82.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 70.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 70.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 72.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 72.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 70.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 70.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 73.96

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

> ui tool show Shell

0.01s - Debugger warning: It seems that frozen modules are being used, which
may  
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off  
0.00s - to python to disable frozen modules.  
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to
disable this validation.  

> show #3 models

> hide #3 models

> torsion #1.2/?:1@N3,C7,C6,C5 73.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 73.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 73.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 74.46

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

> torsion #1.2/?:1@N3,C7,C6,C5 74.46

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

> torsion #1.2/?:1@N3,C7,C6,C5 77.46

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

> torsion #1.2/?:1@N3,C7,C6,C5 77.46

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

> torsion #1.2/?:1@N3,C7,C6,C5 66.46

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

> torsion #1.2/?:1@N3,C7,C6,C5 66.46

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

> torsion #1.2/?:1@N3,C7,C6,C5 71.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 71.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 75.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 75.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 86.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 86.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 86.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 86.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 83.46

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

> torsion #1.2/?:1@N3,C7,C6,C5 83.46

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

> torsion #1.2/?:1@N3,C7,C6,C5 81.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 81.96

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

> torsion #1.2/?:1@N3,C7,C6,C5 88.46

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




OpenGL version: 3.3.0 NVIDIA 529.08
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.13.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.7.22
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.12
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.2
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7rc202311140124
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7rc1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.1
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.12
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    et-xmlfile: 1.1.0
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.44.0
    funcparserlib: 1.0.1
    glfw: 2.6.2
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.0
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.7
    numpy: 1.25.1
    openpyxl: 3.1.2
    openvr: 1.23.701
    packaging: 23.2
    pandas: 2.0.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.0.0
    prompt-toolkit: 3.0.41
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynmrstar: 3.3.2
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.4.1
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    seaborn: 0.12.2
    Send2Trash: 1.8.2
    SEQCROW: 1.7.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.3
    traitlets: 5.9.0
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.10
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

Change History (5)

comment:1 by Tristan Croll, 2 years ago 

Saving the session to .cxs and then reloading it (in the same ChimeraX
instance) did fix it, though.

On Mon, Dec 18, 2023 at 4:57 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>

comment:2 by Tristan Croll, 2 years ago 

Minimal reproduction test case:

{{{
open C1CN(CCN1CCCN2C(=O)N3C=CC=CC3=N2)C4=CC(=CC=C4)Cl fromDatabase smiles
open C1CN(CCN1CCCN2C(=O)N3C=CC=CC3=N2)C4=CC(=CC=C4)Cl fromDatabase smiles
setattr #2 residue chain_id A
view matrix models #2,1,0,0,-0.96656,0,1,0,-3.8786,0,0,1,-0.67812
combine #1,2
close #1,2
ui mousemode right "bond rotation"
}}}

... then right-click and drag on any bond in the "?" chain.

On Mon, Dec 18, 2023 at 5:02 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>

comment:3 by Eric Pettersen, 2 years ago

Cc: Eric Pettersen added
Component: Unassigned → General Controls
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Mouse modes goes bananas

comment:4 by Eric Pettersen, 2 years ago

Also, combining structures with blank IDs with structures with non-blank IDs is problematic, because the only atom spec chain ID that matches a blank chain ID is "/?", which actually matches any chain ID. This probably the cause of the "Must specify exactly 4 atoms for 'torsion' command; you specified 8" message, the /? matching both ligands.

I have changed the "combine" command in the daily build to remap any blank IDs in addition to remapping conflicting IDs.

comment:5 by Tom Goddard, 2 years ago

Resolution: → fixed
Status: assigned → closed

Fixed the stuck mouse mode in ChimeraX 1.8 daily builds, not in 1.7.

The bond rotation mouse mode gave an error when the mouse button was released and that caused the mouse mode code to fail to exit that mode. I now catch mouse up errors and make sure the mouse is not left in that mode.

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