Opened 3 years ago

Closed 3 years ago

#8320 closed defect (fixed)

volume multiply: local variable 'v0' referenced before assignment

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-56-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.dev202301132048 (2023-01-13 20:48:04 UTC)
Description
Log:
Startup Messages  
---  
notes | /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/arrays/__init__.py:32: UserWarning: load_libarrays is no
longer required to link libarrays.Please instead import chimerax.arrays  
warnings.warn(  
/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/arrays/__init__.py:32: UserWarning: load_libarrays is no
longer required to link libarrays.Please instead import chimerax.arrays  
warnings.warn(  
  

> 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: 1.6.dev202301132048 (2023-01-13)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde demo crystal_intro

> set selectionWidth 4

before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #1  
---  
Chain | Description | UniProt  
A | predicted microcompartment protein | A5N734_CLOK5 75-304  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description | UniProt  
1.2/A | predicted microcompartment protein | A5N734_CLOK5 75-304  
  

WARNING: multiple experimental reflection datasets found:  
(dataset) FOBS, SIGFOBS,  
(dataset) IOBS, SIGIOBS,  
(dataset) DANO, SIGDANO,  
(dataset) F(+), SIGF(+), F(-), SIGF(-),  
(dataset) I(+), SIGI(+), I(-), SIGI(-)  
Automatically choosing "(dataset) FOBS, SIGFOBS".  

Launching live xmap mgr took 0.8569817543029785 seconds.  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,36,34, pixel 0.723, shown at
level 0.0947, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,36,34, pixel 0.723, shown at
level -0.0569,0.0569, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 36,36,34, pixel 0.723,
shown at level 0.345, step 1, values float32  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 12 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 36,36,34, pixel 0.723,
shown at level 0.305, step 1, values float32  
Loaded crystallographic demo: PDB ID 3io0  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim pause

> isolde sim stop

Sim termination reason: None  
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 #1

3348 atoms, 3371 bonds, 229 residues, 30 models selected  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> alphafold match #1

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold A5N734 from
https://alphafold.ebi.ac.uk/files/AF-A5N734-F1-model_v4.cif  
1 AlphaFold model found using UniProt identifier: A5N734 (chain A)  
AlphaFold prediction matching before.pdb  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
A | A5N734 | A5N734_CLOK5 | 0.35 | 230 | 229 | 100  
  
Opened 1 AlphaFold model  

> matchmaker #2.1 to #1.2

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 before.pdb, chain A (#1.2) with AlphaFold A5N734_CLOK5 chain A,
chain A (#2.1), sequence alignment score = 1128.8  
RMSD between 229 pruned atom pairs is 0.356 angstroms; (across all 229 pairs:
0.356)  
  

> color #2.1 bychain

> color #2.1 byhetero

> color modify #2.1 hue + 50

ISOLDE: attempting to load PAE matrix for model #2.1 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 #2.1 uniprotId A5N734 plot false

Fetching compressed AlphaFold PAE A5N734 from
https://alphafold.ebi.ac.uk/files/AF-A5N734-F1-predicted_aligned_error_v4.json  

> isolde restrain distances "#1.2/A" templateAtoms "#2.1/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...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 22 residues in
model #2.1 to IUPAC-IUB standards.  

> isolde restrain torsions #1.2/A templateResidues #2.1/A adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20

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

> close #1.2.9

> close #1.2.3

> hide #!2 models

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> select clear

[Repeated 1 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
Unable to flip peptide bond after 50 rounds. Giving up.  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde cisflip sel

Performing cis<\-->trans flip for 1 residues  

> isolde sim stop

Sim termination reason: None  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/tcroll/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 752, in _sim_end_cb  
self._adr_sim_end_cb()  
File "/home/tcroll/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 868, in
_adr_sim_end_cb  
restraints = adrm.intra_restraints(self.sim_construct.all_atoms)  
File "/home/tcroll/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/molobject.py", line 2978, in intra_restraints  
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))  
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'  
  
Error processing trigger "sim terminated":  
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'  
  
File "/home/tcroll/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/molobject.py", line 2978, in intra_restraints  
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))  
  
See log for complete Python traceback.  
  
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  

> select #1

3348 atoms, 3371 bonds, 229 residues, 29 models selected  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
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 sim start sel

ISOLDE: started sim  

> isolde sim pause

> isolde sim resume

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> isolde sim start sel

ISOLDE: started sim  

> select clear

> st

> st first

> isolde sim pause

> st

[Repeated 1 time(s)]

> isolde sim resume

> isolde sim pause

> st

[Repeated 20 time(s)]

> isolde sim resume

> isolde sim pause

> st

[Repeated 3 time(s)]

> isolde sim resume

> isolde sim pause

> st

[Repeated 24 time(s)]

> isolde sim resume

> st

[Repeated 23 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> st

[Repeated 9 time(s)]

> isolde sim pause

> st

[Repeated 6 time(s)]

> isolde sim resume

> isolde sim pause

> st

[Repeated 1 time(s)]

> isolde sim resume

> isolde sim pause

> st

[Repeated 3 time(s)]

> isolde sim resume

> isolde sim pause

> st

[Repeated 11 time(s)]

> isolde sim resume

> isolde sim pause

> st

[Repeated 15 time(s)]

> isolde sim resume

> isolde sim pause

> st

[Repeated 19 time(s)]

> isolde sim resume

> isolde sim pause

> st

[Repeated 8 time(s)]

> isolde sim resume

> isolde sim pause

> st

[Repeated 2 time(s)]

> isolde sim resume

> isolde sim pause

> st

[Repeated 15 time(s)]

> isolde sim resume

> isolde sim pause

> st

[Repeated 1 time(s)]

> isolde sim resume

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim pause

> st

[Repeated 45 time(s)]

> isolde sim resume

> st

[Repeated 4 time(s)]

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1

3348 atoms, 3371 bonds, 229 residues, 30 models selected  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

Sim termination reason: None  
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 sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> al NA

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> st

[Repeated 18 time(s)]

> aw

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> st

[Repeated 23 time(s)]

> aw

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> st

[Repeated 2 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

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

> st

[Repeated 2 time(s)]

> aw

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> st

[Repeated 3 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

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

> st

[Repeated 2 time(s)]

> aw

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> st

[Repeated 2 time(s)]

> aw

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

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

> delete sel

> al NA

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

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

> st

[Repeated 5 time(s)]

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

Deleting Crystallographic maps(3io0-sf.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_29  
Deleting (LIVE) MDFF potential  

> isolde demo crystal_intro

before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #1  
---  
Chain | Description | UniProt  
A | predicted microcompartment protein | A5N734_CLOK5 75-304  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description | UniProt  
1.2/A | predicted microcompartment protein | A5N734_CLOK5 75-304  
  

WARNING: multiple experimental reflection datasets found:  
(dataset) FOBS, SIGFOBS,  
(dataset) IOBS, SIGIOBS,  
(dataset) DANO, SIGDANO,  
(dataset) F(+), SIGF(+), F(-), SIGF(-),  
(dataset) I(+), SIGI(+), I(-), SIGI(-)  
Automatically choosing "(dataset) FOBS, SIGFOBS".  

Launching live xmap mgr took 0.7036983966827393 seconds.  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,36,34, pixel 0.723, shown at
level 0.095, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,36,34, pixel 0.723, shown at
level -0.0573,0.0573, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 36,36,34, pixel 0.723,
shown at level 0.346, step 1, values float32  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 12 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 36,36,34, pixel 0.723,
shown at level 0.305, step 1, values float32  
Loaded crystallographic demo: PDB ID 3io0  

> select clear

> close #1

Deleting Crystallographic maps(3io0-sf.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_29  
Deleting (LIVE) MDFF potential  

> open 6w4e

Summary of feedback from opening 6w4e fetched from pdb  
---  
warnings | Atom HAC is not in the residue template for 17F /A:415  
Atom HAC is not in the residue template for 17F /A:416  
Atom HAC is not in the residue template for 17F /A:422  
Atom HAC is not in the residue template for 17F /D:628  
Atom HAC is not in the residue template for 17F /D:629  
4 messages similar to the above omitted  
Too many hydrogens missing from residue template(s) to warn about  
notes | Fetching compressed mmCIF 6w4e from
http://files.rcsb.org/download/6w4e.cif  
Fetching CCD PCW from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/PCW/PCW.cif  
Fetching CCD 17F from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/17F/17F.cif  
Fetching CCD GSP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GSP/GSP.cif  
  
6w4e title:  
NMR-driven structure of KRAS4B-GTP homodimer on a lipid bilayer nanodisc [more
info...]  
  
Chain information for 6w4e  
---  
Chain | Description | UniProt  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.1/D 1.2/D 1.3/D
1.4/D 1.5/D 1.6/D 1.7/D 1.8/D 1.9/D 1.10/D 1.11/D 1.12/D 1.13/D 1.14/D 1.15/D
1.16/D 1.17/D 1.18/D 1.19/D 1.20/D | Apolipoprotein A-I | APOA1_HUMAN 201-398
399-596  
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.12/B
1.13/B 1.14/B 1.15/B 1.16/B 1.17/B 1.18/B 1.19/B 1.20/B 1.1/C 1.2/C 1.3/C
1.4/C 1.5/C 1.6/C 1.7/C 1.8/C 1.9/C 1.10/C 1.11/C 1.12/C 1.13/C 1.14/C 1.15/C
1.16/C 1.17/C 1.18/C 1.19/C 1.20/C | GTPase KRas | RASK_HUMAN 2-185  
  

> close #1.2-20

> delete /B

> close #1

> open 6w4e

Summary of feedback from opening 6w4e fetched from pdb  
---  
warnings | Atom HAC is not in the residue template for 17F /A:415  
Atom HAC is not in the residue template for 17F /A:416  
Atom HAC is not in the residue template for 17F /A:422  
Atom HAC is not in the residue template for 17F /D:628  
Atom HAC is not in the residue template for 17F /D:629  
4 messages similar to the above omitted  
Too many hydrogens missing from residue template(s) to warn about  
  
6w4e title:  
NMR-driven structure of KRAS4B-GTP homodimer on a lipid bilayer nanodisc [more
info...]  
  
Chain information for 6w4e  
---  
Chain | Description | UniProt  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.1/D 1.2/D 1.3/D
1.4/D 1.5/D 1.6/D 1.7/D 1.8/D 1.9/D 1.10/D 1.11/D 1.12/D 1.13/D 1.14/D 1.15/D
1.16/D 1.17/D 1.18/D 1.19/D 1.20/D | Apolipoprotein A-I | APOA1_HUMAN 201-398
399-596  
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.12/B
1.13/B 1.14/B 1.15/B 1.16/B 1.17/B 1.18/B 1.19/B 1.20/B 1.1/C 1.2/C 1.3/C
1.4/C 1.5/C 1.6/C 1.7/C 1.8/C 1.9/C 1.10/C 1.11/C 1.12/C 1.13/C 1.14/C 1.15/C
1.16/C 1.17/C 1.18/C 1.19/C 1.20/C | GTPase KRas | RASK_HUMAN 2-185  
  

> close #1.2-20

> select /B

2364 atoms, 2377 bonds, 1 pseudobond, 195 residues, 2 models selected  

> delete /B&protein

> delete /C&protein

> delete sel

> open /home/tcroll/structure_dump/terazosin/2ybe/2ybe_rebuilt.pdb

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

> close #2

> open /home/tcroll/Downloads/6w8c_rebuild.pdb

Chain information for 6w8c_rebuild.pdb #2  
---  
Chain | Description  
A B | No description available  
  

> select #1

8374 atoms, 8348 bonds, 476 residues, 2 models selected  

> ui mousemode right "translate selected atoms"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 61 residues in model #1.1 to IUPAC-IUB
standards.  
6w4e title:  
NMR-driven structure of KRAS4B-GTP homodimer on a lipid bilayer nanodisc [more
info...]  
  
Chain information for 6w4e  
---  
Chain | Description | UniProt  
3.2/A 3.2/D | Apolipoprotein A-I | APOA1_HUMAN 201-398 399-596  
  
Non-standard residues in 6w4e #3.2  
---  
17F —
O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine
(1,2-Dioleoyl-sn-glycero-3-phospho-L-serine)  
PCW — 1,2-dioleoyl-Sn-glycero-3-phosphocholine
((Z,Z)-4-hydroxy-N,N,N-trimethyl-10-oxo-7-[(1-oxo-9-octadecenyl)oxy]-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium-4-oxide)  
  

> addh #1

No structures specified  

> addh #3

Summary of feedback from adding hydrogens to 6w4e #3.2  
---  
notes | Termini for 6w4e (#3.2) chain A determined from SEQRES records  
Termini for 6w4e (#3.2) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 6w4e #3.2/A LEU 201,
6w4e #3.2/D LEU 399  
Chain-final residues that are actual C termini: 6w4e #3.2/A ASN 398, 6w4e
#3.2/D ASN 596  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue 6w4e #3.2/A ASN 398  
Missing OXT added to C-terminal residue 6w4e #3.2/D ASN 596  
474 hydrogen bonds  
8736 hydrogens added  
  
Loading residue template for 17F from internal database  
Loading residue template for PCW from internal database  
Deleted the following atoms from residue PCW A401: H38, H18, H21  

> select up

138 atoms, 137 bonds, 1 residue, 1 model selected  

> show sel

Deleted the following atoms from residue PCW D627: H38, H18, H21  
Deleted the following atoms from residue PCW D626: H18, H21, H38  
Deleted the following atoms from residue PCW D625: H21, H18, H38  
Deleted the following atoms from residue PCW D624: H18, H38, H21  
Deleted the following atoms from residue PCW D623: H21, H18, H38  
Deleted the following atoms from residue PCW D622: H38, H21, H18  
Deleted the following atoms from residue PCW D621: H38, H18, H21  
Deleted the following atoms from residue PCW D620: H18, H21, H38  
Deleted the following atoms from residue PCW D619: H18, H21, H38  
Deleted the following atoms from residue PCW D618: H21, H38, H18  
Deleted the following atoms from residue PCW D617: H18, H38, H21  
Deleted the following atoms from residue PCW D616: H21, H38, H18  
Deleted the following atoms from residue PCW D615: H38, H21, H18  
Deleted the following atoms from residue PCW D614: H18, H38, H21  
Deleted the following atoms from residue PCW D613: H18, H21, H38  
Deleted the following atoms from residue PCW D612: H21, H38, H18  
Deleted the following atoms from residue PCW D611: H21, H18, H38  
Deleted the following atoms from residue PCW D610: H21, H38, H18  
Deleted the following atoms from residue PCW D609: H38, H21, H18  
Deleted the following atoms from residue PCW D608: H38, H21, H18  
Deleted the following atoms from residue PCW D607: H18, H21, H38  
Deleted the following atoms from residue PCW D606: H38, H18, H21  
Deleted the following atoms from residue PCW D605: H18, H38, H21  
Deleted the following atoms from residue PCW D604: H21, H38, H18  
Deleted the following atoms from residue PCW D603: H38, H18, H21  
Deleted the following atoms from residue PCW D602: H21, H18, H38  
Deleted the following atoms from residue PCW D601: H18, H21, H38  
Deleted the following atoms from residue PCW C217: H21, H38, H18  
Deleted the following atoms from residue PCW C216: H21, H38, H18  
Deleted the following atoms from residue PCW C212: H38, H18, H21  
Deleted the following atoms from residue PCW C211: H18, H38, H21  
Deleted the following atoms from residue PCW C210: H21, H18, H38  
Deleted the following atoms from residue PCW C209: H18, H21, H38  
Deleted the following atoms from residue PCW C208: H38, H18, H21  
Deleted the following atoms from residue PCW C207: H38, H18, H21  
Deleted the following atoms from residue PCW C206: H38, H18, H21  
Deleted the following atoms from residue PCW C205: H18, H38, H21  
Deleted the following atoms from residue PCW C204: H18, H21, H38  
Deleted the following atoms from residue PCW C203: H18, H21, H38  
Deleted the following atoms from residue PCW B208: H21, H38, H18  
Deleted the following atoms from residue PCW B207: H21, H38, H18  
Deleted the following atoms from residue PCW B206: H18, H38, H21  
Deleted the following atoms from residue PCW B205: H18, H21, H38  
Deleted the following atoms from residue PCW B204: H18, H38, H21  
Deleted the following atoms from residue PCW B203: H38, H21, H18  
Deleted the following atoms from residue PCW A421: H38, H18, H21  
Deleted the following atoms from residue PCW A420: H38, H21, H18  
Deleted the following atoms from residue PCW A419: H38, H18, H21  
Deleted the following atoms from residue PCW A418: H18, H38, H21  
Deleted the following atoms from residue PCW A417: H18, H38, H21  
Deleted the following atoms from residue PCW A414: H18, H21, H38  
Deleted the following atoms from residue PCW A413: H18, H21, H38  
Deleted the following atoms from residue PCW A412: H21, H38, H18  
Deleted the following atoms from residue PCW A411: H21, H18, H38  
Deleted the following atoms from residue PCW A410: H18, H21, H38  
Deleted the following atoms from residue PCW A409: H21, H18, H38  
Deleted the following atoms from residue PCW A408: H18, H38, H21  
Deleted the following atoms from residue PCW A407: H38, H21, H18  
Deleted the following atoms from residue PCW A406: H21, H38, H18  
Deleted the following atoms from residue PCW A405: H18, H38, H21  
Deleted the following atoms from residue PCW A404: H38, H21, H18  
Deleted the following atoms from residue PCW A403: H18, H38, H21  
Deleted the following atoms from residue PCW A402: H38, H18, H21  

> select up

138 atoms, 137 bonds, 1 residue, 1 model selected  

> show sel

Deleted the following atoms from residue 17F A415: HC26, HC36, HC38, HC48,
HC24, HC67, HC46, HC37, HC63, HC44, HC22, HC35, HC41, HC14, HC21, HC45, HC5,
HC57, HC15, HC61, HC32, HC65, HC25, HC58, HC7, HC50, HC49, HC10, HC17, HC11,
HC23, HC27, HC52, HC31, HC43, HC39, HC51, HAC, HC13, HC2, HC3, HC, HC28, HC68,
HC19, HC55, HC18, HC53, HC54, HC34, HC64, HC62, HC47, HC16, HC4, HC12, HC40,
HC1, HC56, HC42, HC66, HC8, HC30, HC33, HC59, HC9, HC6, HC60, HC20, HC69, HC29  

> select up

130 atoms, 129 bonds, 1 residue, 1 model selected  

> show sel

> select up

131 atoms, 130 bonds, 1 residue, 1 model selected  

> isolde parameterise sel override true

Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-
daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmpu4ad2o0m/ante.in.mol2 -fi mol2 -o /tmp/tmpu4ad2o0m/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n  
(17F) ``  
(17F) `Welcome to antechamber 20.0: molecular input file processor.`  
(17F) ``  
(17F) `Info: Finished reading file (/tmp/tmpu4ad2o0m/ante.in.mol2); atoms read
(131), bonds read (130).`  
(17F) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(17F) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(17F) ``  
(17F) ``  
(17F) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(17F) `Info: Total number of electrons: 432; net charge: -1`  
(17F) ``  
(17F) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in
-o sqm.out`  
(17F) ``  
(17F) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-
chimerax-daily/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`  
(17F) ``  
(17F) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(17F) ``  
Charges for residue 17F determined  
OpenMM ffXML file 17F written to the current working directory.  
New template added to forcefield as USER_17F. 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.  
Deleted the following atoms from residue 17F D632: HC6, HC7, HC8, HC34, HC53,
HC65, HC43, HC52, HC54, HC9, HC51, HC18, HAC, HC59, HC41, HC48, HC63, HC30,
HC2, HC15, HC35, HC66, HC19, HC60, HC, HC16, HC44, HC20, HC61, HC68, HC50,
HC45, HC38, HC17, HC21, HC39, HC62, HC14, HC40, HC64, HC32, HC1, HC3, HC47,
HC5, HC55, HC4, HC33, HC10, HC22, HC26, HC11, HC42, HC23, HC56, HC27, HC49,
HC29, HC36, HC31, HC67, HC12, HC46, HC37, HC24, HC57, HC28, HC13, HC69, HC25,
HC58  
Deleted the following atoms from residue 17F D631: HC24, HC25, HC26, HC27,
HC38, HC51, HC8, HC3, HAC, HC1, HC20, HC53, HC50, HC40, HC65, HC9, HC41, HC34,
HC21, HC54, HC30, HC35, HC10, HC67, HC22, HC55, HC4, HC11, HC49, HC69, HC23,
HC44, HC52, HC6, HC7, HC, HC60, HC64, HC62, HC61, HC63, HC5, HC16, HC39, HC46,
HC12, HC33, HC28, HC57, HC47, HC29, HC13, HC32, HC17, HC66, HC45, HC58, HC42,
HC15, HC48, HC14, HC18, HC43, HC36, HC31, HC59, HC68, HC56, HC37, HC2, HC19  
Deleted the following atoms from residue 17F D630: HC29, HC39, HC66, HC35,
HC3, HC13, HC21, HC23, HC12, HC42, HC44, HC26, HC6, HC32, HC58, HC51, HC18,
HC55, HC22, HC59, HC65, HC45, HC7, HC40, HC56, HC34, HC60, HC46, HC8, HC30,
HC67, HC57, HC24, HC61, HC47, HC25, HAC, HC9, HC41, HC20, HC69, HC19, HC33,
HC36, HC27, HC49, HC43, HC, HC48, HC1, HC38, HC64, HC10, HC14, HC63, HC28,
HC11, HC4, HC2, HC15, HC52, HC5, HC17, HC16, HC62, HC54, HC53, HC50, HC68,
HC31, HC37  
Deleted the following atoms from residue 17F D629: HC5, HC12, HC13, HC2, HC14,
HC15, HC22, HC68, HC33, HC36, HC31, HC49, HC8, HC42, HC56, HC38, HC57, HC43,
HC9, HC66, HC58, HC3, HC40, HC1, HC44, HC29, HC10, HC51, HC11, HC23, HC59,
HC41, HC45, HC4, HC39, HC28, HC24, HC52, HC25, HC34, HC69, HC53, HC54, HC55,
HC19, HC, HC60, HC37, HC46, HC64, HC16, HC63, HAC, HC26, HC20, HC32, HC61,
HC50, HC27, HC47, HC65, HC17, HC21, HC62, HC6, HC48, HC67, HC18, HC35, HC30,
HC7  
Deleted the following atoms from residue 17F D628: HC3, HC18, HC13, HC1, HC25,
HC15, HC9, HC4, HC11, HC14, HC35, HC58, HC62, HC44, HC6, HC48, HC10, HC59,
HC26, HC32, HC63, HC45, HC7, HC20, HC60, HC21, HC46, HC8, HC5, HC12, HC34,
HC61, HC50, HC43, HC30, HC27, HC51, HC64, HC31, HC68, HC67, HC47, HC17, HC22,
HC49, HC65, HC54, HC24, HC66, HC36, HC40, HC69, HC55, HC19, HC37, HC41, HC2,
HC52, HC56, HC33, HC38, HAC, HC42, HC, HC28, HC16, HC29, HC53, HC57, HC39,
HC23  
Deleted the following atoms from residue 17F C219: HC9, HC10, HC4, HC11, HC44,
HC69, HC37, HC59, HC31, HC38, HC35, HC32, HC21, HC6, HC45, HC36, HC51, HC22,
HC65, HC58, HC7, HC23, HC48, HC8, HC67, HC34, HC54, HC61, HC24, HC55, HC17,
HC13, HC2, HC47, HC18, HC39, HC14, HC19, HC20, HC50, HC62, HC29, HC25, HC3,
HC56, HC1, HC64, HC57, HC40, HC28, HC63, HC26, HC30, HC46, HC33, HC15, HC41,
HC66, HC52, HC27, HAC, HC, HC53, HC60, HC12, HC5, HC16, HC42, HC68, HC49, HC43  
Deleted the following atoms from residue 17F C218: HC1, HC40, HC42, HC28,
HC57, HC29, HC68, HC15, HC16, HC30, HC4, HC11, HC69, HC43, HC27, HC37, HC8,
HC5, HC12, HC64, HC38, HC56, HC50, HC13, HC39, HC46, HC66, HC58, HC3, HC47,
HC52, HC14, HC48, HC59, HC33, HC23, HC31, HC24, HC25, HAC, HC9, HC10, HC53,
HC26, HC45, HC49, HC19, HC2, HC, HC54, HC55, HC60, HC34, HC44, HC20, HC61,
HC65, HC17, HC51, HC35, HC32, HC21, HC62, HC6, HC67, HC18, HC36, HC41, HC22,
HC63, HC7  
Deleted the following atoms from residue 17F C215: HC, HC44, HC52, HC53, HC54,
HC56, HC55, HC57, HC1, HAC, HC13, HC47, HC62, HC29, HC9, HC33, HC40, HC65,
HC41, HC10, HC14, HC63, HC30, HC20, HC4, HC11, HC2, HC15, HC36, HC37, HC24,
HC5, HC12, HC32, HC16, HC50, HC45, HC25, HC26, HC27, HC28, HC64, HC3, HC58,
HC60, HC6, HC51, HC17, HC21, HC39, HC68, HC34, HC48, HC61, HC18, HC59, HC22,
HC35, HC42, HC7, HC49, HC43, HC19, HC23, HC31, HC46, HC8, HC69, HC38, HC66,
HC67  
Deleted the following atoms from residue 17F C214: HC19, HC20, HC21, HC22,
HC23, HC63, HC29, HC50, HC7, HC6, HC59, HC45, HC2, HC15, HC38, HC60, HC39,
HC16, HC28, HC61, HC34, HC17, HC35, HC42, HC64, HC62, HC48, HC65, HC43, HC18,
HC31, HC69, HC44, HC32, HC51, HC26, HC66, HC41, HC49, HC, HC46, HC47, HAC,
HC55, HC11, HC10, HC4, HC52, HC27, HC56, HC8, HC33, HC12, HC5, HC67, HC40,
HC24, HC53, HC57, HC37, HC9, HC13, HC30, HC25, HC54, HC58, HC3, HC1, HC36,
HC14, HC68  
Deleted the following atoms from residue 17F C213: HAC, HC26, HC32, HC49,
HC42, HC43, HC45, HC2, HC34, HC46, HC37, HC53, HC9, HC54, HC6, HC3, HC27,
HC10, HC33, HC69, HC64, HC40, HC55, HC7, HC41, HC24, HC4, HC11, HC23, HC52,
HC30, HC56, HC8, HC66, HC12, HC5, HC36, HC31, HC50, HC19, HC20, HC25, HC47,
HC38, HC48, HC21, HC22, HC57, HC61, HC67, HC13, HC17, HC58, HC62, HC44, HC1,
HC39, HC14, HC51, HC18, HC28, HC59, HC63, HC29, HC15, HC65, HC68, HC, HC35,
HC60, HC16  
Deleted the following atoms from residue 17F B211: HC28, HC29, HC30, HC68,
HC1, HC56, HC42, HC63, HC4, HC57, HC12, HC49, HC64, HC38, HC60, HC53, HC9,
HC13, HC39, HC43, HC66, HC54, HAC, HC58, HC10, HC14, HC40, HC44, HC2, HC51,
HC59, HC55, HC, HC11, HC15, HC41, HC45, HC24, HC31, HC25, HC26, HC27, HC8,
HC61, HC52, HC33, HC69, HC16, HC3, HC34, HC46, HC62, HC20, HC65, HC17, HC50,
HC35, HC47, HC32, HC5, HC21, HC67, HC18, HC36, HC48, HC6, HC22, HC7, HC37,
HC19, HC23  
Deleted the following atoms from residue 17F B210: HC19, HC20, HC21, HC22,
HC50, HC60, HC67, HC3, HC6, HC7, HC14, HC64, HC18, HC44, HAC, HC48, HC62,
HC63, HC15, HC56, HC45, HC57, HC16, HC34, HC46, HC1, HC39, HC68, HC53, HC17,
HC35, HC47, HC29, HC30, HC51, HC66, HC, HC25, HC54, HC43, HC40, HC42, HC61,
HC10, HC36, HC55, HC26, HC65, HC33, HC11, HC37, HC41, HC4, HC23, HC27, HC8,
HC49, HC31, HC52, HC5, HC12, HC38, HC58, HC24, HC32, HC28, HC59, HC2, HC13,
HC69, HC9  
Deleted the following atoms from residue 17F B209: HC19, HC20, HC22, HC21,
HC32, HC55, HC35, HC36, HC62, HC37, HC27, HC49, HC60, HC5, HC12, HC42, HC16,
HC46, HC28, HC54, HAC, HC65, HC13, HC17, HC43, HC47, HC29, HC14, HC67, HC18,
HC44, HC48, HC30, HC51, HC4, HC58, HC15, HC1, HC45, HC61, HC23, HC24, HC25,
HC66, HC56, HC40, HC26, HC33, HC39, HC2, HC8, HC31, HC53, HC34, HC, HC38,
HC64, HC9, HC59, HC50, HC52, HC6, HC63, HC3, HC69, HC10, HC57, HC7, HC68,
HC11, HC41  
Deleted the following atoms from residue 17F A422: HC10, HC22, HC33, HC41,
HC24, HC60, HC69, HC9, HC17, HC30, HC31, HC21, HC66, HC56, HC68, HC59, HC16,
HC35, HC14, HC18, HC23, HC50, HC32, HC3, HC42, HC4, HC7, HC62, HC55, HC48,
HC15, HC37, HC26, HC46, HC29, HC45, HC8, HC, HC19, HC61, HC25, HC38, HC65,
HC36, HC40, HC51, HC2, HC44, HC5, HC49, HC58, HC47, HC57, HC43, HC13, HC1,
HC64, HC34, HC12, HC20, HC54, HC28, HC11, HC63, HC52, HAC, HC39, HC6, HC53,
HC27, HC67  
Deleted the following atoms from residue 17F A416: HC17, HC1, HC49, HC54,
HC50, HC43, HC31, HC53, HC69, HC5, HC41, HC58, HC64, HC27, HC34, HC46, HC63,
HC15, HC48, HC25, HC66, HC38, HC13, HC21, HC9, HC62, HC52, HC, HC18, HC39,
HC40, HC3, HC28, HC35, HC68, HC55, HAC, HC10, HC6, HC14, HC22, HC30, HC32,
HC42, HC26, HC60, HC20, HC2, HC65, HC29, HC4, HC11, HC59, HC44, HC8, HC51,
HC37, HC45, HC33, HC57, HC24, HC23, HC67, HC7, HC19, HC12, HC56, HC61, HC36,
HC16, HC47  

> usage molmap

molmap atoms resolution [gridSpacing gridSpacing] [edgePadding a number]
[onGrid a density map specifier] [cutoffRange a number] [sigmaFactor a number]
[balls true or false] [symmetry symmetry] [center center point] [axis an axis
vector] [coordinateSystem a coordinate-system] [displayThreshold a number]
[replace true or false] [showDialog true or false]  
— Compute a map by placing Gaussians at atom positions  
resolution: a number > 0  
gridSpacing: a number > 0  

> molmap #2 resolution 6 gridSpacing 1

Missing or invalid "resolution" argument: Expected a number  

> molmap #2 6 gridSpacing 1

Opened 6w8c_rebuild.pdb map 6 as #4, grid size 112,120,121, pixel 1, shown at
level 0.0924, step 1, values float32  

> volume multiply #6 -1

Expected a keyword  

> usage vol mult

volume multiply volumes [onGrid a density maps specifier] [boundingGrid true
or false] [gridSubregion map region] [gridStep map step] [spacing 1 or 3
floats] [valueType numeric value type] [hideMaps true or false] [subregion map
region] [step map step] [modelId modelId] [inPlace true or false]
[scaleFactors scaleFactors]  
— Multiply maps pointwise  
modelId: a model id  
scaleFactors: fromlevels or some numbers  

> usage vol scale

volume scale volumes [shift a number] [factor a number] [sd a number] [rms a
number] [valueType numeric value type] [subregion map region] [step map step]
[modelId modelId]  
— Scale and shift map values  
modelId: a model id  

> usage vol

volume [volumes] [style style] [change change] [show] [hide] [toggle] [close
close] [level level] [rmsLevel rmsLevel] [sdLevel sdLevel] [encloseVolume
encloseVolume] [fastEncloseVolume fastEncloseVolume] [color color] [brightness
a number] [transparency a number] [appearance appearance] [nameAppearance a
text string] [nameForget nameForget] [step map step] [region map region]
[expandSinglePlane true or false] [origin 1 or 3 floats] [originIndex 1 or 3
floats] [voxelSize 1 or 3 floats] [planes planes
x|y|z[,<start>[,<end>[,<increment>[,<depth>]]]]] [dumpHeader true or false]
[pickable true or false] [symmetry symmetry] [center center point]
[centerIndex 1 or 3 floats] [axis an axis vector] [coordinateSystem a
coordinate-system] [dataCacheSize a number] [showOnOpen true or false]
[voxelLimitForOpen a number] [showPlane true or false] [voxelLimitForPlane a
number] [showOutlineBox true or false] [outlineBoxRgb a color]
[limitVoxelCount true or false] [voxelLimit a number] [colorMode colorMode]
[colormapOnGpu true or false] [colormapSize an integer] [colormapExtendLeft
true or false] [colormapExtendRight true or false] [backingColor backingColor]
[blendOnGpu true or false] [projectionMode projectionMode] [planeSpacing
planeSpacing] [fullRegionOnGpu true or false] [btCorrection true or false]
[minimalTextureMemory true or false] [maximumIntensityProjection true or
false] [linearInterpolation true or false] [dimTransparency true or false]
[dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting
true or false] [twoSidedLighting true or false] [flipNormals true or false]
[subdivideSurface true or false] [subdivisionLevels an integer]
[surfaceSmoothing true or false] [smoothingIterations an integer]
[smoothingFactor a number] [squareMesh true or false] [capFaces true or false]
[boxFaces true or false] [orthoplanes orthoplanes] [positionPlanes
positionPlanes] [tiltedSlab true or false] [tiltedSlabAxis an axis vector]
[tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount
an integer] [imageMode imageMode] [calculateSurfaces true or false]  
— set volume model parameters, display style and colors  
style: one of image, mesh, solid, or surface  
change: one of image or surface  
close: one of image or surface  
level: some numbers, repeatable  
rmsLevel: some numbers, repeatable  
sdLevel: some numbers, repeatable  
encloseVolume: some numbers  
fastEncloseVolume: some numbers  
color: a color, repeatable  
appearance: one of Airways, airways, Airways II, Black & White, Bone + Skin,
Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
Bone  
nameForget: one of Airways, airways, Airways II, Black & White, Bone + Skin,
Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
Bone  
colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16,
la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8,
rgba12, rgba16, rgba4, or rgba8  
backingColor: a color or none  
projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, or auto  
planeSpacing: one of max, mean, or min or a number  
orthoplanes: one of off, xy, xyz, xz, or yz  
positionPlanes: some integers  
imageMode: one of box faces, full region, orthoplanes, or tilted slab  
Subcommands are:

  * volume add
  * volume bin
  * volume boxes
  * volume channels
  * volume copy
  * volume cover
  * volume erase
  * volume falloff
  * volume flatten
  * volume flip
  * volume fourier
  * volume gaussian
  * volume laplacian
  * volume localCorrelation
  * volume mask
  * volume maximum
  * volume median
  * volume minimum
  * volume morph
  * volume multiply
  * volume new
  * volume octant
  * volume ~octant
  * volume onesmask
  * volume permuteAxes
  * volume resample
  * volume ridges
  * volume scale
  * volume settings
  * volume splitbyzone
  * volume subtract
  * volume threshold
  * volume tile
  * volume unbend
  * volume unroll
  * volume unzone
  * volume zone

  

> usage vol mult

volume multiply volumes [onGrid a density maps specifier] [boundingGrid true
or false] [gridSubregion map region] [gridStep map step] [spacing 1 or 3
floats] [valueType numeric value type] [hideMaps true or false] [subregion map
region] [step map step] [modelId modelId] [inPlace true or false]
[scaleFactors scaleFactors]  
— Multiply maps pointwise  
modelId: a model id  
scaleFactors: fromlevels or some numbers  

> volume multiply #6 scaleFactors -1

Number of scale factors does not match number of volumes  

> volume multiply #4 scaleFactors -1

Opened 6w8c_rebuild.pdb map 6 resampled as #5, grid size 112,120,121, pixel 1,
shown at step 1, values float32  

> close #5

> volume multiply #4 scaleFactors -1 inPlace true

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_filter/vopcommand.py", line 360, in volume_multiply  
rv = combine_op(volumes, 'multiply', on_grid, bounding_grid, subregion, step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_filter/vopcommand.py", line 388, in combine_op  
cv = [combine_operation(volumes, operation, subregion, step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_filter/vopcommand.py", line 388, in <listcomp>  
cv = [combine_operation(volumes, operation, subregion, step,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_filter/vopcommand.py", line 451, in combine_operation  
rv.copy_settings_from(v0, copy_region = False, copy_xform = False, copy_colors
= False)  
UnboundLocalError: local variable 'v0' referenced before assignment  
  
UnboundLocalError: local variable 'v0' referenced before assignment  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map_filter/vopcommand.py", line 451, in combine_operation  
rv.copy_settings_from(v0, copy_region = False, copy_xform = False, copy_colors
= False)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 515.86.01
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.4.0, Qt 6.4.0
Qt runtime version: 6.4.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: XPS 8950
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
Cache Size: 25600 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi        15Gi       7.6Gi       1.2Gi       8.2Gi        14Gi
	Swap:          2.0Gi       1.4Gi       565Mi

Graphics:
	0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3070 Lite Hash Rate] [10de:2488] (rev a1)	
	Subsystem: Dell GA104 [GeForce RTX 3070 Lite Hash Rate] [1028:c903]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.5.8
    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.8
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.5
    ChimeraX-AtomicLibrary: 10.0.1
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.20.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.dev202301132048
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3.1
    ChimeraX-DockPrep: 1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.11
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.11
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.8
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10
    ChimeraX-PDB: 2.6.12
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.26
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.6
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comm: 0.1.2
    contourpy: 1.0.7
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.5
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.0.0
    ipykernel: 6.19.2
    ipython: 8.7.0
    ipython-genutils: 0.2.0
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 7.4.8
    jupyter-core: 5.1.3
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.6.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.8
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.6.2
    prompt-toolkit: 3.0.36
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.4.0
    PyQt6-Qt6: 6.4.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.2
    python-dateutil: 2.8.2
    pytz: 2022.7.1
    pyzmq: 25.0.0
    qtconsole: 5.4.0
    QtPy: 2.3.0
    RandomWords: 0.4.0
    rdkit-pypi: 2022.9.2
    requests: 2.28.1
    scipy: 1.9.3
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
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    sphinxcontrib-applehelp: 1.0.3
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
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    sphinxcontrib-jsmath: 1.0.1
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    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.10.10
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    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (4)

comment:1 by pett, 3 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → volume multiply: local variable 'v0' referenced before assignment

comment:2 by Tom Goddard, 3 years ago

The "volume multiply" command multiplies two or more maps point-wise. It does not scale a map. For that use the "volume scale" command.

I'll fix "volume multiply" so it gives a sensible error message if you only specify one map.

comment:3 by Tom Goddard, 3 years ago

The "volume multiply" command allows specifying just one map, it just fails with the "inPlace true" option. I fixed that so it works. Still using the "volume scale" command is the way to go. Oh, I see "volume scale" does not have an inPlace option. Should fix that.

comment:4 by Tom Goddard, 3 years ago

Resolution: → fixed
Status: assigned → closed

Fixed "volume multiply" with one map and inPlace true.

Made a new ticket #8325 to add an inPlace option to the "volume scale" command.

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