Permission denied writing command history

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.3rc202112030319 (2021-12-03 03:19:12 UTC)
Description
PermissionError on running a command, trying to replace some temporary file.

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: 1.3rc202112030319 (2021-12-03)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7kry format mmcif fromDatabase pdb structureFactors true

Summary of feedback from opening 7kry fetched from pdb  
---  
notes | Resolution: 2.5531158017926043  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,38,30, pixel
0.804,0.804,0.834, shown at level 0.273, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,38,30, pixel
0.804,0.804,0.834, shown at level -0.0891,0.0891, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_8 as #1.1.1.4, grid size 50,38,30, pixel
0.804,0.804,0.834, shown at level 0.465, step 1, values float32  
7kry title:  
Co-crystal structure of α glucosidase with compound 11 [more info...]  
  
Chain information for 7kry  
---  
Chain | Description | UniProt  
1.2/A 1.2/C | Neutral alpha-glucosidase AB | GANAB_MOUSE  
1.2/B 1.2/D | Glucosidase 2 subunit β | GLU2B_MOUSE  
  
Non-standard residues in 7kry #1.2  
---  
CA — calcium ion  
EDO — 1,2-ethanediol (ethylene glycol)  
P6G — hexaethylene glycol (polyethylene glycol PEG400)  
PEG — di(hydroxyethyl)ether  
SO4 — sulfate ion  
X8Y —
(1S,2S,3R,4S,5S)-5-({6-[(4-azido-2-nitrophenyl)amino]hexyl}amino)-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol  
  
7kry mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> addh

Summary of feedback from adding hydrogens to 7kry #1.2  
---  
warnings | Not adding hydrogens to /A GLN 68 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A GLU 107 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 109 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 164 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 182 CB because it is missing heavy-atom bond
partners  
29 messages similar to the above omitted  
notes | Termini for 7kry (#1.2) chain A determined from SEQRES records  
Termini for 7kry (#1.2) chain B determined from SEQRES records  
Termini for 7kry (#1.2) chain C determined from SEQRES records  
Termini for 7kry (#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 VAL 33, /A GLY 246,
/A THR 370, /B SER 34, /C VAL 33, /C GLU 244, /C THR 370, /D SER 34  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A PRO 184, /A ASN 350, /A
ARG 966, /B ARG 117, /C ARG 185, /C ASN 350, /C ARG 966, /D ARG 117  
3256 hydrogen bonds  
Adding 'H' to /A VAL 33  
Adding 'H' to /A GLY 246  
Adding 'H' to /A THR 370  
Adding 'H' to /B SER 34  
Adding 'H' to /C VAL 33  
3 messages similar to the above omitted  
/A ARG 966 is not terminus, removing H atom from 'C'  
/B ARG 117 is not terminus, removing H atom from 'C'  
/C ARG 966 is not terminus, removing H atom from 'C'  
/D ARG 117 is not terminus, removing H atom from 'C'  
15280 hydrogens added  
  

> view :X8Y

> view /A:X8Y

> select /A:1001@C9

1 atom, 1 residue, 1 model selected  

> select up

67 atoms, 68 bonds, 1 residue, 1 model selected  

> deh :X8Y&H

Unknown command: deh :X8Y&H  

> delete :X8Y&H

> addh template true

Summary of feedback from adding hydrogens to 7kry #1.2  
---  
warnings | Not adding hydrogens to /A GLN 68 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A GLU 107 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 109 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 164 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 182 CB because it is missing heavy-atom bond
partners  
29 messages similar to the above omitted  
notes | Termini for 7kry (#1.2) chain A determined from SEQRES records  
Termini for 7kry (#1.2) chain B determined from SEQRES records  
Termini for 7kry (#1.2) chain C determined from SEQRES records  
Termini for 7kry (#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 VAL 33, /A GLY 246,
/A THR 370, /B SER 34, /C VAL 33, /C GLU 244, /C THR 370, /D SER 34  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A PRO 184, /A ASN 350, /A
ARG 966, /B ARG 117, /C ARG 185, /C ASN 350, /C ARG 966, /D ARG 117  
2593 hydrogen bonds  
/A ARG 966 is not terminus, removing H atom from 'C'  
/B ARG 117 is not terminus, removing H atom from 'C'  
/C ARG 966 is not terminus, removing H atom from 'C'  
/D ARG 117 is not terminus, removing H atom from 'C'  
64 hydrogens added  
  

> select /A:1001@HN3

1 atom, 1 residue, 1 model selected  

> delete sel

> select /A:1001@C12

1 atom, 1 residue, 1 model selected  

> 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\tmpprk85zwb\ante.in.mol2 -fi mol2 -o
C:\Users\tristan\AppData\Local\Temp\tmpprk85zwb\ante.out.mol2 -fo mol2 -c bcc
-nc -3 -j 5 -s 2 -dr n  
(X8Y) ``  
(X8Y) `Welcome to antechamber 20.0: molecular input file processor.`  
(X8Y) ``  
(X8Y) `Info: Finished reading file
(C:\Users\tristan\AppData\Local\Temp\tmpprk85zwb\ante.in.mol2); atoms read
(63), bonds read (64).`  
(X8Y) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) ``  
(X8Y) ``  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) `Info: Total number of electrons: 246; net charge: -3`  
(X8Y) ``  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) `/usr/bin/antechamber: Fatal Error!`  
(X8Y) `Cannot properly run ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out".`  
Failure running ANTECHAMBER for residue X8Y Check reply log for details  

> 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\tmpw_6opega\ante.in.mol2 -fi mol2 -o
C:\Users\tristan\AppData\Local\Temp\tmpw_6opega\ante.out.mol2 -fo mol2 -c bcc
-nc -3 -j 5 -s 2 -dr n  
(X8Y) ``  
(X8Y) `Welcome to antechamber 20.0: molecular input file processor.`  
(X8Y) ``  
(X8Y) `Info: Finished reading file
(C:\Users\tristan\AppData\Local\Temp\tmpw_6opega\ante.in.mol2); atoms read
(63), bonds read (64).`  
(X8Y) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) ``  
(X8Y) ``  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) `Info: Total number of electrons: 246; net charge: -3`  
(X8Y) ``  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) `/usr/bin/antechamber: Fatal Error!`  
(X8Y) `Cannot properly run ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out".`  
Failure running ANTECHAMBER for residue X8Y Check reply log for details  

> 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\tmpyth6z7qs\ante.in.mol2 -fi mol2 -o
C:\Users\tristan\AppData\Local\Temp\tmpyth6z7qs\ante.out.mol2 -fo mol2 -c bcc
-nc -3 -j 5 -s 2 -dr n  
(X8Y) ``  
(X8Y) `Welcome to antechamber 20.0: molecular input file processor.`  
(X8Y) ``  
(X8Y) `Info: Finished reading file
(C:\Users\tristan\AppData\Local\Temp\tmpyth6z7qs\ante.in.mol2); atoms read
(63), bonds read (64).`  
(X8Y) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) ``  
(X8Y) ``  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) `Info: Total number of electrons: 246; net charge: -3`  
(X8Y) ``  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) `/usr/bin/antechamber: Fatal Error!`  
(X8Y) `Cannot properly run ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out".`  
Failure running ANTECHAMBER for residue X8Y Check reply log for details  

> 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\tmpm8o6n3nt\ante.in.mol2 -fi mol2 -o
C:\Users\tristan\AppData\Local\Temp\tmpm8o6n3nt\ante.out.mol2 -fo mol2 -c bcc
-nc -3 -j 5 -s 2 -dr n  
(X8Y) ``  
(X8Y) `Welcome to antechamber 20.0: molecular input file processor.`  
(X8Y) ``  
(X8Y) `Info: Finished reading file
(C:\Users\tristan\AppData\Local\Temp\tmpm8o6n3nt\ante.in.mol2); atoms read
(63), bonds read (64).`  
(X8Y) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) ``  
(X8Y) ``  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) `Info: Total number of electrons: 246; net charge: -3`  
(X8Y) ``  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) `/usr/bin/antechamber: Fatal Error!`  
(X8Y) `Cannot properly run ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out".`  
Failure running ANTECHAMBER for residue X8Y Check reply log for details  

> al X8Y

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 133 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 50,38,30, pixel
0.804,0.804,0.834, shown at level 0.287, step 1, values float32  

place_ligand() was called with use_md_template=True, but no suitable template
was found. This command has been ignored.  

Done loading forcefield  

> 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\tmpd94hap3v\ante.in.mol2 -fi mol2 -o
C:\Users\tristan\AppData\Local\Temp\tmpd94hap3v\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(X8Y) ``  
(X8Y) `Welcome to antechamber 20.0: molecular input file processor.`  
(X8Y) ``  
(X8Y) `Info: Finished reading file
(C:\Users\tristan\AppData\Local\Temp\tmpd94hap3v\ante.in.mol2); atoms read
(62), bonds read (63).`  
(X8Y) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) ``  
(X8Y) ``  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) `Info: Total number of electrons: 242; net charge: 0`  
(X8Y) ``  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) ``  
(X8Y) `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`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) ``  
(X8Y) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(X8Y) `bash.exe: warning: could not find /tmp, please create!`  
(X8Y) ``  
Charges for residue X8Y determined  
OpenMM ffXML file X8Y written to the current working directory.  
New template added to forcefield as USER_X8Y. 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

62 atoms, 63 bonds, 1 residue, 1 model selected  

> select up

14411 atoms, 14346 bonds, 1134 residues, 1 model selected  

> select up

62 atoms, 63 bonds, 1 residue, 1 model selected  

> delete sel

Loading residue template for EDO from internal database  
Loading residue template for P6G from internal database  
Loading residue template for PEG from internal database  
Loading residue template for SO4 from internal database  
Deleted the following atoms from residue X8Y A1001: HN1, HC8, HC18, HO2, HC21,
HC14, HC13, HC12, HC9, HC10, HC15, HC4, HC22, HC19, HO3, HC3, HC7, HC6, HC16,
HC11, HN, HC17, HO1, HN2, HC5, HC20, HO, HO4, HC2, HC, HC1  
Deleted the following atoms from residue X8Y C1102: HC12, HC11, HC13, HN2,
HC19, HO4, HC10, HC5, HC9, HC2, HC1, HC16, HC20, HO1, HO3, HC21, HC, HC3, HC4,
HC8, HC6, HN, HC22, HO, HC15, HO2, HC17, HN3, HC18, HC14, HC7, HN1  

> view /A:X8Y

ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  

> set bgColor white

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

> close #1

Deleting Crystallographic maps (7kry-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_8  
Deleting (LIVE) MDFF potential  

> open 6pwz structureFactors true

Summary of feedback from opening 6pwz fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
intensity_meas, intensity_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 6pwz from
http://files.rcsb.org/download/6pwz.cif  
Fetching CCD P6D from http://ligand-expo.rcsb.org/reports/P/P6D/P6D.cif  
Fetching compressed 6pwz structure factors from
http://files.rcsb.org/download/6pwz-sf.cif  
Resolution: 2.468007301565645  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,34,32, pixel 0.781,0.785,0.8,
shown at level 0.248, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,34,32, pixel 0.781,0.785,0.8,
shown at level -0.103,0.103, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_2 as #1.1.1.4, grid size 36,34,32, pixel
0.781,0.785,0.8, shown at level 0.243, step 1, values float32  
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.5, grid size 36,34,32,
pixel 0.781,0.785,0.8, shown at level -0.352,0.352, step 1, values float32  
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.6, grid size 36,34,32, pixel
0.781,0.785,0.8, shown at level -0.903,0.903, step 1, values float32  
6pwz title:  
Crystal structure of human uridine-cytidine kinase 2 complexed with
2'-azidocytidine [more info...]  
  
Chain information for 6pwz  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H | Uridine-cytidine kinase 2 |
UCK2_HUMAN  
  
Non-standard residues in 6pwz #1.2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
P6D — 2'-azidocytidine  
PO4 — phosphate ion  
  
6pwz mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
Removed all altlocs in #1.2 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 94 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.7, grid size 36,34,32, pixel
0.781,0.785,0.8, shown at level 0.232, step 1, values float32  

> view /A:P6D

No objects specified.  

> select :P6D

57 atoms, 60 bonds, 3 residues, 1 model selected  

> view /B:P6D

No objects specified.  

> view /C:P6D

No objects specified.  

> view /DS:P6D

No objects specified.  

> view /D:P6D

> select :P6D

57 atoms, 60 bonds, 3 residues, 1 model selected  

> close #1

Deleting Crystallographic maps (6pwz-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_2  
Deleting (LIVE) MDFF potential  

> open 6n54 structureFactors true

Summary of feedback from opening 6n54 fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
intensity_meas, intensity_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 6n54 from
http://files.rcsb.org/download/6n54.cif  
Fetching CCD KEA from http://ligand-expo.rcsb.org/reports/K/KEA/KEA.cif  
Fetching compressed 6n54 structure factors from
http://files.rcsb.org/download/6n54-sf.cif  
Resolution: 2.4239053670789183  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 32,34,32, pixel
0.807,0.785,0.765, shown at level 0.316, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 32,34,32, pixel
0.807,0.785,0.765, shown at level -0.0808,0.0808, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_4 as #1.1.1.4, grid size 32,34,32, pixel
0.807,0.785,0.765, shown at level 0.303, step 1, values float32  
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.5, grid size 32,34,32,
pixel 0.807,0.785,0.765, shown at level -0.224,0.224, step 1, values float32  
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.6, grid size 32,34,32, pixel
0.807,0.785,0.765, shown at level -0.626,0.626, step 1, values float32  
6n54 title:  
Crystal structure of human uridine-cytidine kinase 2 complexed with
2'-azidocytidine monophosphate [more info...]  
  
Chain information for 6n54  
---  
Chain | Description | UniProt  
1.2/A 1.2/B | Uridine-cytidine kinase 2 | UCK2_HUMAN  
  
Non-standard residues in 6n54 #1.2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
KEA — 2'-azido-2'-deoxycytidine 5'-(dihydrogen phosphate) (2'-azidocytidine
monophosphate)  
MG — magnesium ion  
PO4 — phosphate ion  
  
6n54 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 32 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.7, grid size 32,34,32, pixel
0.807,0.785,0.765, shown at level 0.275, step 1, values float32  

> view /A:KEA

> view /B:KEA

> close #1

Deleting Crystallographic maps (6n54-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_4  
Deleting (LIVE) MDFF potential  

> open 6n55 structureFactors true

Summary of feedback from opening 6n55 fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
intensity_meas, intensity_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 6n55 from
http://files.rcsb.org/download/6n55.cif  
Fetching CCD UZ0 from http://ligand-expo.rcsb.org/reports/U/UZ0/UZ0.cif  
Fetching compressed 6n55 structure factors from
http://files.rcsb.org/download/6n55-sf.cif  
Resolution: 3.085022189417611  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 30,26,24, pixel 0.966,1.02,1.02,
shown at level 0.174, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 30,26,24, pixel 0.966,1.02,1.02,
shown at level -0.0875,0.0875, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_32 as #1.1.1.4, grid size 30,26,24, pixel
0.966,1.02,1.02, shown at level 0.385, step 1, values float32  
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.5, grid size 30,26,24,
pixel 0.966,1.02,1.02, shown at level -0.245,0.245, step 1, values float32  
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.6, grid size 30,26,24, pixel
0.966,1.02,1.02, shown at level -0.583,0.583, step 1, values float32  
6n55 title:  
Crystal structure of human uridine-cytidine kinase 2 complexed with
2'-azidouridine [more info...]  
  
Chain information for 6n55  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H | Uridine-cytidine kinase 2 |
UCK2_HUMAN  
  
Non-standard residues in 6n55 #1.2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
PO4 — phosphate ion  
UZ0 — 2'-azido-2'-deoxyuridine  
  
6n55 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
Removed all altlocs in #1.2 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 106 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.7, grid size 30,26,24, pixel
0.966,1.02,1.02, shown at level 0.193, step 1, values float32  

> view /A:UZ0

No objects specified.  

> select :UZ0

57 atoms, 60 bonds, 3 residues, 1 model selected  

> close #1

Deleting Crystallographic maps (6n55-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_32  
Deleting (LIVE) MDFF potential  

> open 6hoc structureFactors true

Summary of feedback from opening 6hoc fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
phase_calc, fom  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 6hoc from
http://files.rcsb.org/download/6hoc.cif  
Fetching CCD GJE from http://ligand-expo.rcsb.org/reports/G/GJE/GJE.cif  
Fetching compressed 6hoc structure factors from
http://files.rcsb.org/download/6hoc-sf.cif  
Resolution: 2.496459726890199  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 34,34,36, pixel 0.76,0.76,0.705,
shown at level 0.436, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 34,34,36, pixel 0.76,0.76,0.705,
shown at level -0.14,0.14, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_1 as #1.1.1.4, grid size 34,34,36, pixel
0.76,0.76,0.705, shown at level 0.616, step 1, values float32  
Opened (STATIC) F_calc_au, phase_calc as #1.1.1.5, grid size 34,34,36, pixel
0.76,0.76,0.705, shown at level -0.832,0.832, step 1, values float32  
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.6, grid size 34,34,36,
pixel 0.76,0.76,0.705, shown at level -0.228,0.228, step 1, values float32  
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.7, grid size 34,34,36, pixel
0.76,0.76,0.705, shown at level -0.695,0.695, step 1, values float32  
6hoc title:  
Transcriptional repressor ETHR from mycobacterium tuberculosis In complex with
BDM44847 [more info...]  
  
Chain information for 6hoc  
---  
Chain | Description | UniProt  
1.2/A | HTH-type transcriptional regulator EthR | ETHR_MYCTO  
  
Non-standard residues in 6hoc #1.2  
---  
GJE — 4-azido-~{N}-[3,3,3-tris(fluoranyl)propyl]benzamide  
  
6hoc mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
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.  
Opened (LIVE) MDFF potential as #1.1.1.8, grid size 34,34,36, pixel
0.76,0.76,0.705, shown at level 0.425, step 1, values float32  

> select :GJE

18 atoms, 18 bonds, 1 residue, 1 model selected  

> addh template true

Summary of feedback from adding hydrogens to 6hoc #1.2  
---  
notes | Termini for 6hoc (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A ARG 25, /A ASP 98  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ASN 93, /A GLU 214  
236 hydrogen bonds  
Adding 'H' to /A ARG 25  
Adding 'H' to /A ASP 98  
/A GLU 214 is not terminus, removing H atom from 'C'  
1469 hydrogens added  
  

> delete sel

> isolde parameterise sel

GJE: number of electrons (132) + formal charge (-3) is odd; cannot compute
charges for radical species using AM1-BCC method  

> select up

27 atoms, 27 bonds, 1 residue, 1 model selected  

> show sel

> isolde parameterise sel netCharge 0

Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\tristan\AppData\Local\Temp\tmp8_u8shar\ante.in.mol2 -fi mol2 -o
C:\Users\tristan\AppData\Local\Temp\tmp8_u8shar\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(GJE) ``  
(GJE) `Welcome to antechamber 20.0: molecular input file processor.`  
(GJE) ``  
(GJE) `Info: Finished reading file
(C:\Users\tristan\AppData\Local\Temp\tmp8_u8shar\ante.in.mol2); atoms read
(27), bonds read (27).`  
(GJE) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(GJE) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(GJE) `bash.exe: warning: could not find /tmp, please create!`  
(GJE) ``  
(GJE) ``  
(GJE) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(GJE) `bash.exe: warning: could not find /tmp, please create!`  
(GJE) `Info: Total number of electrons: 132; net charge: 0`  
(GJE) ``  
(GJE) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(GJE) `bash.exe: warning: could not find /tmp, please create!`  
(GJE) ``  
(GJE) `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`  
(GJE) `bash.exe: warning: could not find /tmp, please create!`  
(GJE) ``  
(GJE) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(GJE) `bash.exe: warning: could not find /tmp, please create!`  
(GJE) ``  
Charges for residue GJE determined  
OpenMM ffXML file GJE written to the current working directory.  
New template added to forcefield as USER_GJE. 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.  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> delete H

> addh

Summary of feedback from adding hydrogens to 6hoc #1.2  
---  
notes | Termini for 6hoc (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A ARG 25, /A ASP 98  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ASN 93, /A GLU 214  
235 hydrogen bonds  
Adding 'H' to /A ARG 25  
Adding 'H' to /A ASP 98  
/A GLU 214 is not terminus, removing H atom from 'C'  
1471 hydrogens added  
  

> select up

30 atoms, 30 bonds, 1 residue, 1 model selected  

> show sel

> delete sel

> isolde parameterise sel netCharge 0

Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\tristan\AppData\Local\Temp\tmpl0uele67\ante.in.mol2 -fi mol2 -o
C:\Users\tristan\AppData\Local\Temp\tmpl0uele67\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(GJE) ``  
(GJE) `Welcome to antechamber 20.0: molecular input file processor.`  
(GJE) ``  
(GJE) `Info: Finished reading file
(C:\Users\tristan\AppData\Local\Temp\tmpl0uele67\ante.in.mol2); atoms read
(27), bonds read (27).`  
(GJE) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(GJE) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(GJE) `bash.exe: warning: could not find /tmp, please create!`  
(GJE) ``  
(GJE) ``  
(GJE) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(GJE) `bash.exe: warning: could not find /tmp, please create!`  
(GJE) `Info: Total number of electrons: 132; net charge: 0`  
(GJE) ``  
(GJE) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(GJE) `bash.exe: warning: could not find /tmp, please create!`  
(GJE) ``  
(GJE) `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`  
(GJE) `bash.exe: warning: could not find /tmp, please create!`  
(GJE) ``  
(GJE) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(GJE) `bash.exe: warning: could not find /tmp, please create!`  
(GJE) ``  
Charges for residue GJE determined  
OpenMM ffXML file GJE written to the current working directory.  
New template added to forcefield as USER_GJE. 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.  
ISOLDE: started sim  

> select clear

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

> close #1

Deleting Crystallographic maps (6hoc-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_1  
Deleting (LIVE) MDFF potential  

> isolde tutorial

> open 6mhz

6mhz title:  
Vanadate trapped Cryo-EM Structure of E.coli LptB2FG Transporter [more
info...]  
  
Chain information for 6mhz #1  
---  
Chain | Description | UniProt  
A B | Lipopolysaccharide export system ATP-binding protein LptB | LPTB_ECOLI  
F | Lipopolysaccharide export system permease protein LptF | LPTF_ECOLI  
G | Lipopolysaccharide export system permease protein LptG | LPTG_ECOLI  
  
Non-standard residues in 6mhz #1  
---  
AOV — adp orthovanadate  
  

> open 9118 fromDatabase emdb

Opened emdb 9118 as #2, grid size 192,192,192, pixel 1.23, shown at level
0.0393, step 1, values float32  

> hide

> cartoon

> color bychain

> color byhetero

> volume #2 level 0.1

> view initial #1

> view matrix models
> #1,0.198,-0.674,0.699,86.9,0.821,0.511,0.260,-63.7,-0.534,0.522,0.655,53.6

> fitmap #1/A,G inMap #2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 98, in __exit__  
os.replace(self._tmp_filename, self.name)  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\tristan\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.14704.tmp'
-> 'C:\\\Users\\\tristan\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
During handling of the above exception, another exception occurred:  
  
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:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 325, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 423, in add  
self._history.enqueue((item, typed))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue  
self.save()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save  
self._history.save(self._queue)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 106, in __exit__  
os.replace(self._tmp_filename, self.name)  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\tristan\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.14704.tmp'
-> 'C:\\\Users\\\tristan\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
Error processing trigger "command started":  
PermissionError: [WinError 5] Access is denied:
'C:\\\Users\\\tristan\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands.14704.tmp'
-> 'C:\\\Users\\\tristan\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\commands'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 106, in __exit__  
os.replace(self._tmp_filename, self.name)  
  
See log for complete Python traceback.  
  
Fit molecule 6mhz (#1) to map emdb 9118 (#2) using 3620 atoms  
average map value = 0.04229, steps = 92  
shifted from previous position = 5.59  
rotated from previous position = 10.6 degrees  
atoms outside contour = 3070, contour level = 0.1  
  
Position of 6mhz (#1) relative to emdb 9118 (#2) coordinates:  
Matrix rotation and translation  
0.20397820 -0.53842290 0.80678158 60.51587984  
0.76323569 0.61057869 0.21678452 -63.39391917  
-0.61177216 0.57024157 0.53603540 70.90289792  
Axis 0.18057178 0.72470126 0.66498264  
Axis point 89.96139317 0.00000000 16.44820834  
Rotation angle (degrees) 79.84552389  
Shift along axis 12.13500315  
  




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: 2.0.8
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    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: 1.31
    ChimeraX-AtomicLibrary: 4.2
    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: 2.6.1
    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: 1.3rc202112030319
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    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
    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: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    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
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    versioneer: 0.21
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Eric Pettersen]

This can happen on Windows if some other process (e.g. virus scanner) has the file open. ChimeraX already retries once to try to get around this issue. I guess I'll have it try a few times before it gives up and throws the error.

[Eric Pettersen]

The code now retries 3 times instead of just once.