Opened 4 years ago

Last modified 4 years ago

#5907 reopened enhancement

Better starting directory when ChimeraX launched by file association

Reported by: Tristan Croll Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Greg Couch, pett
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.3rc202112030319 (2021-12-03 03:19:12 UTC)
Description
Opened a ChimeraX session file by double-clicking in the Windows File Manager. Resultant working directory is c:\windows\system32. Doesn't seem ideal - wouldn't it be better to set it to the directory the session file is in?

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

> open "C:\\\Users\\\tristan\\\OneDrive - University of
> Cambridge\\\Structures\\\Pu_Qian\\\r_palustris\\\PucA-LH2\\\working.cxs"

Opened zflip.mrc as #1.1.1.1, grid size 270,270,270, pixel 0.65, shown at
level 0.014, step 1, values float32  
Opened zflip.mrc gaussian as #1.1.1.2, grid size 270,270,270, pixel 0.66,
shown at level 0.0108, step 1, values float32  
Opened zflip.mrc zone as #5, grid size 270,270,270, pixel 0.66, shown at level
0.0233, step 1, values float32  
Opened pucA_mask.mrc as #6, grid size 270,270,270, pixel 0.66, shown at level
0.000575, step 1, values float32  
Log from Fri Dec 10 12:52:03 2021

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

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

> cd "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/Pu_Qian/r_palustris/PucA-LH2"

Current working directory is: C:\Users\tristan\OneDrive - University of
Cambridge\Structures\Pu_Qian\r_palustris\PucA-LH2  

> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/Pu_Qian/r_palustris/PucA-LH2/pucA-LH2GCMX-
> ldao_real_space_refined_004.cif" "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/Pu_Qian/r_palustris/PucA-LH2/zflip.mrc"

Summary of feedback from opening C:/Users/tristan/OneDrive - University of
Cambridge/Structures/Pu_Qian/r_palustris/PucA-LH2/pucA-LH2GCMX-
ldao_real_space_refined_004.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 735  
Missing entity information. Treating each chain as a separate entity.  
Invalid residue range for struct_conf "4": invalid entity "B", near line 190  
Invalid residue range for struct_conf "5": invalid entity "B", near line 191  
Invalid residue range for struct_conf "6": invalid entity "C", near line 192  
Invalid residue range for struct_conf "7": invalid entity "C", near line 193  
Invalid residue range for struct_conf "8": invalid entity "C", near line 194  
27 messages similar to the above omitted  
Atom H is not in the residue template for GLU /S:4  
Atom C1 is not in the residue template for RDP /B:1797  
Atom C1 is not in the residue template for RDP /D:1797  
Atom C1 is not in the residue template for RDP /F:1797  
Atom C1 is not in the residue template for RDP /H:1797  
Atom C1 is not in the residue template for RDP /J:1797  
4 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 13455  
Skipping chem_comp category: Missing column 'type' near line 13613  
Skipping chem_comp category: Missing column 'type' near line 14518  
Skipping chem_comp category: Missing column 'type' near line 15207  
notes | Fetching CCD LDA from http://ligand-
expo.rcsb.org/reports/L/LDA/LDA.cif  
Fetching CCD RDP from http://ligand-expo.rcsb.org/reports/R/RDP/RDP.cif  
  
Chain information for pucA-LH2GCMX-ldao_real_space_refined_004.cif #1  
---  
Chain | Description  
A C E G I K M O Q | No description available  
B D F H J L N P R | No description available  
S | No description available  
  
Opened zflip.mrc as #2, grid size 270,270,270, pixel 0.66, shown at level
0.0156, step 2, values float32  

> clipper associate #2 toModel #1

Opened zflip.mrc as #1.1.1.1, grid size 270,270,270, pixel 0.66, shown at
level 0.0247, step 1, values float32  
Chain information for pucA-LH2GCMX-ldao_real_space_refined_004.cif  
---  
Chain | Description  
1.2/A 1.2/C 1.2/E 1.2/G 1.2/I 1.2/K 1.2/M 1.2/O 1.2/Q | No description
available  
1.2/B 1.2/D 1.2/F 1.2/H 1.2/J 1.2/L 1.2/N 1.2/P 1.2/R | No description
available  
1.2/S | No description available  
  

> addh

Summary of feedback from adding hydrogens to pucA-LH2GCMX-
ldao_real_space_refined_004.cif #1.2  
---  
warning | Unknown hybridization for atom (C4) of residue type RDP; not adding
hydrogens to it  
notes | No usable SEQRES records for pucA-LH2GCMX-
ldao_real_space_refined_004.cif (#1.2) chain A; guessing termini instead  
No usable SEQRES records for pucA-LH2GCMX-ldao_real_space_refined_004.cif
(#1.2) chain B; guessing termini instead  
No usable SEQRES records for pucA-LH2GCMX-ldao_real_space_refined_004.cif
(#1.2) chain C; guessing termini instead  
No usable SEQRES records for pucA-LH2GCMX-ldao_real_space_refined_004.cif
(#1.2) chain D; guessing termini instead  
No usable SEQRES records for pucA-LH2GCMX-ldao_real_space_refined_004.cif
(#1.2) chain E; guessing termini instead  
14 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A CXM 1, /B ALA 2, /C CXM
1, /D ALA 2, /E CXM 1, /F ALA 2, /G CXM 1, /H ALA 2, /I CXM 1, /J ALA 2, /K
CXM 1, /L ALA 2, /M CXM 1, /N ALA 2, /O CXM 1, /P ALA 2, /Q CXM 1, /R ALA 2  
Chain-initial residues that are not actual N termini: /S GLU 4  
Chain-final residues that are actual C termini: /S ILE 97  
Chain-final residues that are not actual C termini: /A ALA 50, /B HIS 47, /C
ALA 50, /D HIS 47, /E ALA 50, /F HIS 47, /G ALA 50, /H HIS 47, /I ALA 50, /J
HIS 47, /K ALA 50, /L HIS 47, /M ALA 50, /N HIS 47, /O ALA 50, /P HIS 47, /Q
ALA 50, /R HIS 47  
852 hydrogen bonds  
/A ALA 50 is not terminus, removing H atom from 'C'  
/B HIS 47 is not terminus, removing H atom from 'C'  
/C ALA 50 is not terminus, removing H atom from 'C'  
/D HIS 47 is not terminus, removing H atom from 'C'  
/E ALA 50 is not terminus, removing H atom from 'C'  
13 messages similar to the above omitted  
10089 hydrogens added  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 35 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  
Loading residue template for LDA from internal database  

> ~hbonds

Deleted the following atoms from residue BCL R1697: MG  
Deleted the following atoms from residue BCL R1598: MG  
Deleted the following atoms from residue BCL Q1702: MG  
Deleted the following atoms from residue BCL Q1502: MG  
Deleted the following atoms from residue BCL P1697: MG  
Deleted the following atoms from residue BCL P1598: MG  
Deleted the following atoms from residue BCL O1702: MG  
Deleted the following atoms from residue BCL O1502: MG  
Deleted the following atoms from residue BCL N1697: MG  
Deleted the following atoms from residue BCL N1598: MG  
Deleted the following atoms from residue BCL M1702: MG  
Deleted the following atoms from residue BCL M1502: MG  
Deleted the following atoms from residue BCL L1697: MG  
Deleted the following atoms from residue BCL L1598: MG  
Deleted the following atoms from residue BCL K1702: MG  
Deleted the following atoms from residue BCL K1502: MG  
Deleted the following atoms from residue BCL J1697: MG  
Deleted the following atoms from residue BCL J1598: MG  
Deleted the following atoms from residue BCL I1702: MG  
Deleted the following atoms from residue BCL I1502: MG  
Deleted the following atoms from residue BCL H1697: MG  
Deleted the following atoms from residue BCL H1598: MG  
Deleted the following atoms from residue BCL G1702: MG  
Deleted the following atoms from residue BCL G1502: MG  
Deleted the following atoms from residue BCL F1598: MG, HGA  
Deleted the following atoms from residue BCL E1702: MG  
Deleted the following atoms from residue BCL E1502: MG  
Deleted the following atoms from residue BCL D1598: MG  
Deleted the following atoms from residue BCL C1702: MG  
Deleted the following atoms from residue BCL C1502: MG  
Deleted the following atoms from residue BCL B1598: MG  
Deleted the following atoms from residue BCL A1702: MG  
Deleted the following atoms from residue BCL A1502: MG  

> 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\tmpm6go_7am\ante.in.mol2 -fi mol2 -o
C:\Users\tristan\AppData\Local\Temp\tmpm6go_7am\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(RDP) ``  
(RDP) `Welcome to antechamber 20.0: molecular input file processor.`  
(RDP) ``  
(RDP) `Info: Finished reading file
(C:\Users\tristan\AppData\Local\Temp\tmpm6go_7am\ante.in.mol2); atoms read
(99), bonds read (98).`  
(RDP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(RDP) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(RDP) `bash.exe: warning: could not find /tmp, please create!`  
(RDP) ``  
(RDP) ``  
(RDP) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(RDP) `bash.exe: warning: could not find /tmp, please create!`  
(RDP) `Info: Total number of electrons: 306; net charge: 0`  
(RDP) ``  
(RDP) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(RDP) `bash.exe: warning: could not find /tmp, please create!`  
(RDP) ``  
(RDP) `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`  
(RDP) `bash.exe: warning: could not find /tmp, please create!`  
(RDP) ``  
(RDP) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(RDP) `bash.exe: warning: could not find /tmp, please create!`  
(RDP) ``  
Charges for residue RDP determined  
OpenMM ffXML file RDP written to the current working directory.  
New template added to forcefield as USER_RDP. 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.  

> delete sel

[Repeated 1 time(s)]

> set bgColor white

> hide HC

> dssp

> select #1

22381 atoms, 22821 bonds, 2 pseudobonds, 1034 residues, 13 models selected  

> select #1

22381 atoms, 22821 bonds, 2 pseudobonds, 1034 residues, 16 models selected  
ISOLDE: started sim  

> select clear

ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 10 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

47 atoms, 46 bonds, 1 residue, 1 model selected  

> delete sel

> st first

> volume gaussian #1 bfactor 50

Opened zflip.mrc gaussian as #2, grid size 270,270,270, pixel 0.66, shown at
step 1, values float32  

> clipper associate #2 toModel #1

Opened zflip.mrc gaussian as #1.1.1.2, grid size 270,270,270, pixel 0.66,
shown at step 1, values float32  

> cs 0.25

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  

> delete sel

> ui tool show "Show Sequence Viewer"

> st /A

Multiple residues selected! Going to the first...  

> select /A

1087 atoms, 1115 bonds, 52 residues, 1 model selected  
ISOLDE: started sim  
ISOLDE: paused sim  

> st

[Repeated 3 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

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

> select /B

965 atoms, 982 bonds, 48 residues, 1 model selected  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select /A,B

2052 atoms, 2097 bonds, 100 residues, 1 model selected  
ISOLDE: started sim  
ISOLDE: paused sim  

> select clear

> st

[Repeated 7 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

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

> st

[Repeated 5 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 3 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 7 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 5 time(s)]ISOLDE: resumed sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> awsf

> select /A,B

2055 atoms, 2099 bonds, 101 residues, 1 model selected  
ISOLDE: started sim  
ISOLDE: paused sim  

> st

[Repeated 4 time(s)]ISOLDE: resumed sim  

> st

[Repeated 47 time(s)]ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
Added a C-terminal OXT to chain B  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save pucA_working.cxs

Taking snapshot of stepper: pucA-LH2GCMX-ldao_real_space_refined_004.cif  

> ui tool show Shell

> select protein&~/S

13798 atoms, 13996 bonds, 864 residues, 1 model selected  

> usage sym

sym structures [symmetry] [center center point] [axis an axis vector]
[coordinateSystem a coordinate-system] [contact a number] [range a number]
[assembly a text string] [copies true or false] [newModel true or false]
[surfaceOnly true or false] [resolution a number] [gridSpacing a number]  
— create model copies  
symmetry: symmetry

sym clear [structures]  
— Remove model copies  

> select clear

> select /A,B

2056 atoms, 2100 bonds, 101 residues, 1 model selected  

> select :BCL

4480 atoms, 4737 bonds, 32 residues, 1 model selected  

> select clear

> select /A,B

2056 atoms, 2100 bonds, 101 residues, 1 model selected  

> select clear

> select /A,B

2056 atoms, 2100 bonds, 101 residues, 1 model selected  
Chain information for ASU #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show "Show Sequence Viewer"

> sym #2 C9 axis 0,0,1 center 89.34,88.99,86.23

> close #3

> ui tool show "Show Sequence Viewer"

> sym #2 C8 axis 0,0,1 center 89.34,88.99,86.23

> close #3

> sym #2 C9 axis 0,0,1 center 89.34,88.99,86.23

> select #1/A,B

2056 atoms, 2100 bonds, 101 residues, 1 model selected  

> hide #!3 models

> show #2 models

> delete #1&~/A,B,S

> hide #2 models

> show #!3 models

> hide #3.1 models

> close #3.1

> select #3

16448 atoms, 16800 bonds, 808 residues, 9 models selected  
ISOLDE: merge models  
Merging models #3.2,#3.3,#3.4,#3.5,#3.6,#3.7,#3.8,#3.9 into #1.2.  
Remapping chain ID A in #3.2 to C  
Remapping chain ID B in #3.2 to D  
Remapping chain ID A in #3.3 to E  
Remapping chain ID B in #3.3 to F  
Remapping chain ID A in #3.4 to G  
Remapping chain ID B in #3.4 to H  
Remapping chain ID A in #3.5 to I  
Remapping chain ID B in #3.5 to J  
Remapping chain ID A in #3.6 to K  
Remapping chain ID B in #3.6 to L  
Remapping chain ID A in #3.7 to M  
Remapping chain ID B in #3.7 to N  
Remapping chain ID A in #3.8 to O  
Remapping chain ID B in #3.8 to P  
Remapping chain ID A in #3.9 to Q  
Remapping chain ID B in #3.9 to R  

> hide #!3 models

> isolde restrain torsions #1&~/S

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

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

> select #1

19979 atoms, 20394 bonds, 1003 residues, 21 models selected  

> isolde restrain distances #1

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

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 6 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1

19979 atoms, 20394 bonds, 1003 residues, 21 models selected  

> rd

> select clear

> st /A

Multiple residues selected! Going to the first...  

> st

[Repeated 45 time(s)]ISOLDE: started sim  

> select clear

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

> st

[Repeated 48 time(s)]

> select :RDP

1782 atoms, 1764 bonds, 18 residues, 10 models selected  

> select /A,B:RDP

990 atoms, 980 bonds, 10 residues, 10 models selected  

> select #1/A,B:RDP

99 atoms, 98 bonds, 1 residue, 1 model selected  

> close #3

> ui mousemode right "translate selected atoms"

> isolde ignore #1&~sel

ISOLDE: currently ignoring 1002 residues in model 1.2  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde ~ignore

ISOLDE: started sim  

> select clear

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

> select up

99 atoms, 98 bonds, 1 residue, 1 model selected  

> close #2

> sym #3 C9 axis 0,0,1 center 89.34,88.99,86.23

> view /D:RDP

> select clear

> close #2

> close #3

> select up

99 atoms, 98 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 1002 residues in model 1.2  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde ~ignore

> select /F:RDP

99 atoms, 98 bonds, 1 residue, 1 model selected  

> view sel

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 1002 residues in model 1.2  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde ~ignore

> select /H:RDP

99 atoms, 98 bonds, 1 residue, 1 model selected  

> view sel

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 1002 residues in model 1.2  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde ~ignore

> select /J:RDP

99 atoms, 98 bonds, 1 residue, 1 model selected  

> view sel

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 1002 residues in model 1.2  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde ~ignore

> select /L:RDP

99 atoms, 98 bonds, 1 residue, 1 model selected  

> view sel

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 1002 residues in model 1.2  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde ~ignore

ISOLDE: started sim  

> select clear

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

> select /N:RDP

99 atoms, 98 bonds, 1 residue, 1 model selected  

> view sel

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 1002 residues in model 1.2  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde ~ignore

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

> select /P:RDP

99 atoms, 98 bonds, 1 residue, 1 model selected  

> view sel

> ui mousemode right "translate selected atoms"

> isolde ignore ~sel

ISOLDE: currently ignoring 1002 residues in model 1.2  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde ~ignore

ISOLDE: started sim  

> select clear

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

> select /R:RDP

99 atoms, 98 bonds, 1 residue, 1 model selected  

> view sel

> ui mousemode right "translate selected atoms"

> select up

966 atoms, 983 bonds, 48 residues, 1 model selected  

> select down

99 atoms, 98 bonds, 1 residue, 1 model selected  

> isolde ignore ~sel

ISOLDE: currently ignoring 1002 residues in model 1.2  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde ~ignore

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

> save working.cxs

Taking snapshot of stepper: pucA-LH2GCMX-ldao_real_space_refined_004.cif  

> select #1

19979 atoms, 20394 bonds, 1003 residues, 21 models selected  

> select clear

> open C:/Users/tristan/Downloads/working.pdb

Chain information for working.pdb #2  
---  
Chain | Description  
A | No description available  
B E I K N Q T W Z | No description available  
D G H M P S V Y | No description available  
O | No description available  
  

> matchmaker #2/A to #1/A

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 pucA-LH2GCMX-ldao_real_space_refined_004.cif, chain A (#1.2) with
working.pdb, chain A (#2), sequence alignment score = 221.9  
RMSD between 48 pruned atom pairs is 0.410 angstroms; (across all 50 pairs:
2.142)  
  

> cartoon #2

> hide #2

> matchmaker #2/O to #1/S

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 pucA-LH2GCMX-ldao_real_space_refined_004.cif, chain S (#1.2) with
working.pdb, chain O (#2), sequence alignment score = 426  
RMSD between 75 pruned atom pairs is 1.016 angstroms; (across all 91 pairs:
1.734)  
  

> show #2/O

> style stick

Changed 41279 atom styles  

> isolde restrain torsions #1/S templateResidues #2/O

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 8 residues in model
#2 to IUPAC-IUB standards.  

> hide #!2 models

> select #1/S

1475 atoms, 1494 bonds, 94 residues, 1 model selected  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  

> show #!2 models

> hide #!2 models

ISOLDE: paused sim  
ISOLDE: resumed sim  

> rt

ISOLDE: paused sim  
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/S

1475 atoms, 1494 bonds, 94 residues, 1 model selected  

> save s.pdb #1 selectedOnly true

> open s.pdb

Summary of feedback from opening s.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 4
THR A 8 1 5  
Start residue of secondary structure not found: HELIX 2 2 PRO A 12 HIS A 37 1
26  
Start residue of secondary structure not found: HELIX 3 3 TRP A 40 ASN A 46 1
7  
Start residue of secondary structure not found: HELIX 4 4 VAL B 11 TYR B 42 1
32  
Start residue of secondary structure not found: HELIX 5 5 ALA C 4 THR C 8 1 5  
31 messages similar to the above omitted  
  
Chain information for s.pdb #3  
---  
Chain | Description  
S | No description available  
  

> sym #3 C9 axis 0,0,1 center 89.34,88.99,86.23

> select #1

19979 atoms, 20394 bonds, 1003 residues, 21 models selected  

> show #4

> hide HC

> usage color bymodel

color [objects] [color [what]] [target characters from 'abcfmprs']
[transparency a number] [halfbond true or false]  
— color objects  
objects: an objects specifier or nothing  
color: a color or one of byatom, bychain, byelement, byhetero, byidentity,
bymodel, bynucleotide, bypolymer, fromatoms, or random  
what: a collection of one of All, atoms, bonds, cartoons, labels, models,
pseudobonds, ribbons, rings, or surfaces  
Subcommands are:

  * color bfactor
  * color byattribute
  * color cylindrical
  * color delete
  * color electrostatic
  * color gradient
  * color height
  * color image
  * color list
  * color modify
  * color name
  * color radial
  * color sample
  * color sequential
  * color show
  * color single
  * color zone

  

> select #4

13275 atoms, 13446 bonds, 846 residues, 10 models selected  

> ~cartoon #4

> cartoon #4

> select clear

> hide #4 models

> show #4.8 models

> select clear

> show #4.1 models

> show #4.2 models

> show #4.3 models

> show #4.4 models

> show #4.5 models

> show #4.6 models

> show #4.7 models

> show #4.9 models

> usage vol mask

volume mask volumes surfaces a surfaces specifier [pad a number] [extend an
integer] [fullMap true or false] [slab slab] [invertMask true or false] [axis
an axis vector] [sandwich true or false] [fillOverlap true or false] [modelId
modelId]  
— Mask a map to a surface  
slab: a number or some numbers  
modelId: a model id  

> usage vol onesmask

volume onesmask surfaces [onGrid a density map specifier] [spacing 1 or 3
floats] [border a number] [valueType numeric value type] [pad a number]
[extend an integer] [fullMap true or false] [slab slab] [invertMask true or
false] [axis an axis vector] [sandwich true or false] [fillOverlap true or
false] [modelId modelId]  
— Make a mask of 1 values for a surface  
slab: a number or some numbers  
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 zone

volume zone volumes nearAtoms an atoms specifier [range a number]
[bondPointSpacing a number] [minimalBounds true or false] [newMap true or
false] [invert true or false] [subregion map region] [step map step] [modelId
modelId]  
— Zero map values beyond a distance range from atoms  
modelId: a model id  

> volume zone #1.1.1.1 nearAtoms #4 range 12 newMap true

Opened zflip.mrc zone as #5, grid size 270,270,270, pixel 0.66, shown at step
1, values float32  

> close #5

> volume zone #1.1.1.1 nearAtoms #4 range 6 newMap true

Opened zflip.mrc zone as #5, grid size 270,270,270, pixel 0.66, shown at step
1, values float32  

> volume gaussian #5 bfactor 200

Opened zflip.mrc zone gaussian as #6, grid size 270,270,270, pixel 0.66, shown
at step 1, values float32  

> volume #6 level 0.000657

> volume #6 level 0.002705

> volume #6 level 0.003279

> volume #6 level 0.0005751

> select clear

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

> clipper spotlight radius 16.00

> clipper spotlight radius 17.00

> clipper spotlight radius 18.00

ISOLDE: started sim  

> hide #!4 models

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

> st

[Repeated 12 time(s)]ISOLDE: started sim  

> select clear

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

> select #1

19979 atoms, 20394 bonds, 1003 residues, 21 models selected  
ISOLDE: started sim  

> select clear

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

> st

[Repeated 23 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> view /A:37

> view #1/A:37

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

> st

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

> rt

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

> st

[Repeated 8 time(s)]ISOLDE: started sim  

> rt

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

> st

[Repeated 14 time(s)]ISOLDE: started sim  

> rt

> isolde sim stop

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

> aw

> isolde sim start sel

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

> rt

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

> delete sel

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

> st

[Repeated 5 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> view

> view #1/B:20

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

> rt

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

> st

[Repeated 37 time(s)]ISOLDE: started sim  

> select clear

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

> st

[Repeated 8 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 16 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

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

> rt

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

> st

[Repeated 33 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 41 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 17 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 15 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 7 time(s)]

> rt

> st

[Repeated 5 time(s)]

> select clear

> st

[Repeated 4 time(s)]

> rt

ISOLDE: started sim  

> select clear

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  

> rt

> st

[Repeated 36 time(s)]ISOLDE: started sim  

> rt

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

> st

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

> st

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

> select clear

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

> st

[Repeated 18 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 59 time(s)]ISOLDE: started sim  
Traceback (most recent call last):  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2096, in _next_rotamer  
target_def = rrm.next_preview(rot)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\molobject.py", line 4438, in next_preview  
return self._incr_preview(rotamer, 1)  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\molobject.py", line 4420, in _incr_preview  
new_target = (current_target + incr) % num_targets  
ZeroDivisionError: integer division or modulo by zero  
  
ZeroDivisionError: integer division or modulo by zero  
  
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\molobject.py", line 4420, in _incr_preview  
new_target = (current_target + incr) % num_targets  
  
See log for complete Python traceback.  
  

> rt

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

> st

[Repeated 18 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 16 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 60 time(s)]ISOLDE: started sim  

> rt

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

> st

[Repeated 8 time(s)]ISOLDE: started sim  

> rt

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

> st

[Repeated 8 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> view #1/A:20

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

> view #1/C:20

> view #1/E:20

> st

[Repeated 16 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 20 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 4 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 10 time(s)]ISOLDE: started sim  

> rt

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

> st

[Repeated 23 time(s)]ISOLDE: started sim  

> select clear

> rt

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

> st

[Repeated 11 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 22 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 4 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 18 time(s)]ISOLDE: started sim  

> rt

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

> st

[Repeated 3 time(s)]ISOLDE: started sim  

> select clear

> rt

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

> st

[Repeated 32 time(s)]ISOLDE: started sim  

> rt

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

> st

[Repeated 34 time(s)]ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> ht ND

Set protonation of HIS #1.2/Q:37 to ND  
ISOLDE: started sim  

> select clear

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

> st

[Repeated 26 time(s)]ISOLDE: started sim  

> rt

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

> rt

> st

[Repeated 32 time(s)]

> select #1&~protein&~:HOH

4671 atoms, 4878 bonds, 36 residues, 21 models selected  

> clipper spotlight radius 17.00

> clipper spotlight radius 16.00

ISOLDE: started sim  

> select clear

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

> show #!6 models

> save pucA_mask.mrc #6

> volume #6 style image region 0,0,0,269,269,269 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"

> volume #6 style surface region 0,0,0,269,269,269 step 1

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

> select #1

19979 atoms, 20394 bonds, 1003 residues, 21 models selected  

> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/Pu_Qian/r_palustris/PucA-LH2/pucA-LH2GCMX-
> ldao_real_space_refined_004.cif"

Summary of feedback from opening C:/Users/tristan/OneDrive - University of
Cambridge/Structures/Pu_Qian/r_palustris/PucA-LH2/pucA-LH2GCMX-
ldao_real_space_refined_004.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 735  
Missing entity information. Treating each chain as a separate entity.  
Invalid residue range for struct_conf "4": invalid entity "B", near line 190  
Invalid residue range for struct_conf "5": invalid entity "B", near line 191  
Invalid residue range for struct_conf "6": invalid entity "C", near line 192  
Invalid residue range for struct_conf "7": invalid entity "C", near line 193  
Invalid residue range for struct_conf "8": invalid entity "C", near line 194  
27 messages similar to the above omitted  
Atom H is not in the residue template for GLU /S:4  
Atom C1 is not in the residue template for RDP /B:1797  
Atom C1 is not in the residue template for RDP /D:1797  
Atom C1 is not in the residue template for RDP /F:1797  
Atom C1 is not in the residue template for RDP /H:1797  
Atom C1 is not in the residue template for RDP /J:1797  
4 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 13455  
Skipping chem_comp category: Missing column 'type' near line 13613  
Skipping chem_comp category: Missing column 'type' near line 14518  
Skipping chem_comp category: Missing column 'type' near line 15207  
  
Chain information for pucA-LH2GCMX-ldao_real_space_refined_004.cif #7  
---  
Chain | Description  
A C E G I K M O Q | No description available  
B D F H J L N P R | No description available  
S | No description available  
  

> hide #7&~:BCL

> select clear

[Repeated 1 time(s)]

> hide #!1 models

> select #7/H

670 atoms, 687 bonds, 36 pseudobonds, 49 residues, 3 models selected  

> select #7/H:1697

140 atoms, 144 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> select #7:1697

840 atoms, 864 bonds, 24 pseudobonds, 6 residues, 2 models selected  

> delete #7&~sel

> show #!1 models

> save working.cxs\

'working.cxs\' has only compression suffix; cannot determine format from
suffix  

> save working.cxs

Taking snapshot of stepper: pucA-LH2GCMX-ldao_real_space_refined_004.cif  
ISOLDE: merge models  
Merging models #7 into #1.2.  
Remapping chain ID H in #7 to T  
Remapping chain ID J in #7 to U  
Remapping chain ID L in #7 to V  
Remapping chain ID N in #7 to W  
Remapping chain ID P in #7 to X  
Remapping chain ID R in #7 to Y  

> hide #!7 models

ISOLDE: stopped sim  
Deleted the following atoms from residue BCL Y1697: MG  
Deleted the following atoms from residue BCL X1697: MG  
Deleted the following atoms from residue BCL W1697: MG  
Deleted the following atoms from residue BCL V1697: MG  
Deleted the following atoms from residue BCL U1697: MG  
Deleted the following atoms from residue BCL T1697: MG  
ISOLDE: started sim  
ISOLDE: paused sim  

> ui mousemode right "translate selected atoms"

> select up

140 atoms, 148 bonds, 1 residue, 1 model selected  
ISOLDE: resumed sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> aw

> isolde sim start sel

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

> select up

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

> delete sel

> volume gaussian #1.1.1.1 bfactor 150

Opened zflip.mrc gaussian as #8, grid size 270,270,270, pixel 0.66, shown at
step 1, values float32  

> close #8

> show #!1.1.1.1 models

ISOLDE: started sim  

> select clear

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

> rt

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

> save working.cxs

Taking snapshot of stepper: pucA-LH2GCMX-ldao_real_space_refined_004.cif  

——— End of log from Fri Dec 10 12:52:03 2021 ———

opened ChimeraX session  

> pwd

Current working directory is: C:\windows\system32  




OpenGL version: 3.3.0 NVIDIA 497.29
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:
    -: imerax-clipper
    -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
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    tables: 3.6.1
    texttable: 1.6.4
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
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    urllib3: 1.26.7
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    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (7)

comment:1 by pett, 4 years ago

Cc: Greg Couch pett added
Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Better starting directory when ChimeraX launched by file association

comment:2 by pett, 4 years ago

Type: defect → enhancement

comment:3 by Tom Goddard, 4 years ago

When I first double click on a *.cxs file in Windows 10 then use ChimeraX command pwd it does give C:\WINDOWS\system32 after asking me to choose ChimeraX as the application to open it with. But then when I close ChimeraX and try again it correctly makes the current directory the location of the *.cxs file. And I can never get it to give the system32 location again. This seems like a bug in Windows because ChimeraX is not setting the current directory when to the file location it is Windows doing that. But Windows does not seem to do it the first time a file suffix is associated with the app.

Do you also observe this behavior where it only fails to set the correct current directory the first time? Or do you get the problem more than once for the same file type?

I don't see a good way for ChimeraX to fix this since it does not know whether it was started by double clicking a file. Normally when ChimeraX is started by double clicking the app ChimeraX sets the current directory to ~/Desktop if it sees that the current directory is \Users\Public\Desktop which is for some reason the default that the Windows icon has it start in. But when double clicking a file it seems to start in C:\WINDOWS\system32 the first time and then if ChimeraX is quit it subsequently is started in the directory containing the file and in neither of those cases does ChimeraX change the current directory. I could make it change the directory to ~/Desktop on start if it is in \WINDOWS\system32. But that won't match where the file is located.

Actually I am not sure how windows starting from a file double click works. My guess would be the app starts and then later Qt gets an open file event. But it may be that the file was given on the command-line. Need to investigate. If it gives it on the command line then I could use that. But when ChimeraX is started from a shell it generally does not change the current directory it started in, and ChimeraX won't know if it was started from a shell (in \WINDOWS\system32) or from a double click.

comment:4 by Tom Goddard, 4 years ago

Resolution: → nonchimerax
Status: assigned → closed

After rebooting Windows 10 I observe the same behavior that double clicking a file (*.cxs, *.pdb, *.mrc, *.ccp4, *.cif) starts ChimeraX with the current directory set to the directory of the file if that file type was previously associated with ChimeraX. Only when the file type is first associated with ChimeraX does it start with current directory C:\WINDOWS\system32.

This looks like a Windows deficiency and only happens when the first file of a give type is opened in ChimeraX, so I am not going to try to work around it.

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

Hmm, yes - you're right. I guess this was the first time I'd ever opened a .cxs file from the File Manager on this PC. But playing around a bit, I noticed that taking the right-click/open with/ChimeraX approach still sets the working directory to C:\WINDOWS\system32. Obviously not likely to be a problem for .cxs files, but perhaps a minor pain if people have multiple associations for .pdb, .cif, etc. and need to specify which program opens them. Probably not worth the effort to handle, though.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 12 January 2022 22:45
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5907: Better starting directory when ChimeraX launched by file association

#5907: Better starting directory when ChimeraX launched by file association
------------------------------------+-------------------------
          Reporter:  Tristan Croll  |      Owner:  Tom Goddard
              Type:  enhancement    |     Status:  closed
          Priority:  normal         |  Milestone:
         Component:  Input/Output   |    Version:
        Resolution:  nonchimerax    |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+-------------------------
Changes (by Tom Goddard):

 * status:  assigned => closed
 * resolution:   => nonchimerax


Comment:

 After rebooting Windows 10 I observe the same behavior that double
 clicking a file (*.cxs, *.pdb, *.mrc, *.ccp4, *.cif) starts ChimeraX with
 the current directory set to the directory of the file if that file type
 was previously associated with ChimeraX.  Only when the file type is first
 associated with ChimeraX does it start with current directory
 C:\WINDOWS\system32.

 This looks like a Windows deficiency and only happens when the first file
 of a give type is opened in ChimeraX, so I am not going to try to work
 around it.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5907#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  6 ; comment:6 by goddard@…, 4 years ago 

Yes, I see right click on the file icon in Windows file browser and choosing Open with... and choosing ChimeraX does always start with the bad current directory C:\WINDOWS\system32.

It starts with the current directory where the file is only when ChimeraX is the default app to open files with that suffix and you simply double click.

Not great.  It would be worth testing if this same bad Windows behavior is in Windows 11.  If it is then maybe I am inclined to reopen this ticket and try to work around it at some point.

comment:7 by Tom Goddard, 4 years ago

Resolution: nonchimerax
Status: closed → reopened

Should test if same behavior in Windows 11.

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