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Opened 2 years ago
Closed 2 years ago
#9567 closed defect (duplicate)
Restore new session in old ChimeraX
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.0-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/lei_zhong/Desktop/A/Lei/AfcQ/ChimeraX/GrsA/GrsA_1amu_Phe_AMP_Pocket_Cartoon.cxs
Log from Sat Aug 12 17:39:09 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/lei_zhong/Desktop/A/Lei/AfcQ/ChimeraX/GraS_1amu_Pocket的副本.cxs
Log from Sat Aug 12 17:31:50 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/lei_zhong/Desktop/A/Lei/AfcQ/ChimeraX/GraS_1amu_Pocket.cxs
Log from Sat Aug 12 13:34:07 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/lei_zhong/Desktop/test.cxs
Log from Fri Aug 11 20:37:37 2023UCSF ChimeraX version: 1.7.dev202308110027
(2023-08-11)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/lei_zhong/test.cxs format session
Log from Fri Aug 11 20:35:56 2023UCSF ChimeraX version: 1.7.dev202308110027
(2023-08-11)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/lei_zhong/Desktop/A/Lei/AfcQ/PyMol/PDB/PheA:GrsA_Phe_AMP_1amu.pse
Unrecognized file suffix '.pse'
> open
> /Users/lei_zhong/Desktop/A/Lei/AfcQ/PyMol/PDB/PheA:GrsA_Phe_AMP_1amu.pdb
PheA:GrsA_Phe_AMP_1amu.pdb title:
Phenylalanine activating domain of gramicidin synthetase 1 In A complex with
amp and phenylalanine [more info...]
Chain information for PheA:GrsA_Phe_AMP_1amu.pdb #1
---
Chain | Description | UniProt
A B | GRSA | GRSA_BACBR 1-556
Non-standard residues in PheA:GrsA_Phe_AMP_1amu.pdb #1
---
AMP — adenosine monophosphate
MG — magnesium ion
PHE — phenylalanine
SO4 — sulfate ion
> save /Users/lei_zhong/test.cxs
——— End of log from Fri Aug 11 20:35:56 2023 ———
opened ChimeraX session
> save /Users/lei_zhong/test.cxs
——— End of log from Fri Aug 11 20:37:37 2023 ———
opened ChimeraX session
> select protein
7897 atoms, 8067 bonds, 3 pseudobonds, 1017 residues, 2 models selected
> select nucleic-acid
Nothing selected
> select C
5123 atoms, 4122 bonds, 1021 residues, 1 model selected
> select ligand
80 atoms, 82 bonds, 6 residues, 1 model selected
> select ::name="SO4"
10 atoms, 8 bonds, 2 residues, 1 model selected
> hide sel atoms
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 138 NE
4 hydrogen bonds found
> select clear
> select ::name="SO4"
10 atoms, 8 bonds, 2 residues, 1 model selected
> hide sel atoms
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 138 NE
4 hydrogen bonds found
> hide sel atoms
> select clear
> hbonds reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 138 NE
2597 hydrogen bonds found
> ~hbonds
> interfaces ~solvent
1 buried areas: B A 520
> ~hbonds
> select ::name="HOH"
569 atoms, 569 residues, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> hide sel atoms
> select
8548 atoms, 8149 bonds, 9 pseudobonds, 1594 residues, 3 models selected
> hide sel atoms
> select clear
> select /A
4281 atoms, 4075 bonds, 4 pseudobonds, 805 residues, 3 models selected
> hide sel cartoons
> select ::name="AMP"
46 atoms, 50 bonds, 2 residues, 1 model selected
> show sel atoms
> select ::name="PHE"
442 atoms, 444 bonds, 40 residues, 1 model selected
> select ::name="PHE"
442 atoms, 444 bonds, 40 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select ligand
80 atoms, 82 bonds, 6 residues, 1 model selected
> show sel atoms
> select ::name="MG"
2 atoms, 2 residues, 1 model selected
> show sel atoms
> select /A
4281 atoms, 4075 bonds, 4 pseudobonds, 805 residues, 3 models selected
> select /B
4267 atoms, 4074 bonds, 5 pseudobonds, 789 residues, 3 models selected
> hide sel cartoons
> show sel cartoons
> cartoon style (#!1 & sel) xsection oval modeHelix default
> cartoon style (#!1 & sel) xsection rectangle modeHelix default
> cartoon style (#!1 & sel & coil) xsection oval
> cartoon style (#!1 & sel) xsection barbell modeHelix default
> cartoon style (#!1 & sel) modeHelix tube sides 20
> cartoon style (#!1 & sel) xsection oval modeHelix default
> show (#!1 & sel) target ab
> hide (#!1 & sel) target a
> show (#!1 & sel-residues & sidechain) target ab
> cartoon hide (#!1 & sel)
> cartoon (#!1 & sel)
> hide (#!1 & sel) target a
> select ligand
80 atoms, 82 bonds, 6 residues, 1 model selected
> show sel atoms
> select /A
4281 atoms, 4075 bonds, 4 pseudobonds, 805 residues, 3 models selected
> show sel atoms
> show sel cartoons
> hide sel atoms
> select ligand
80 atoms, 82 bonds, 6 residues, 1 model selected
> show sel atoms
> select /B
4267 atoms, 4074 bonds, 5 pseudobonds, 789 residues, 3 models selected
> hide sel cartoons
> select /A
4281 atoms, 4075 bonds, 4 pseudobonds, 805 residues, 3 models selected
> surface (#!1 & sel)
> surface style mesh
> surface style solid
> surface style dot
> surface hidePatches (#!1 & sel)
> select ::name="MG"
2 atoms, 2 residues, 1 model selected
> show sel atoms
> select /A
4281 atoms, 4075 bonds, 4 pseudobonds, 805 residues, 3 models selected
> color (#!1 & sel) light gray
> select clear
> undo
[Repeated 1 time(s)]
> select clear
> select /A
4281 atoms, 4075 bonds, 4 pseudobonds, 805 residues, 3 models selected
> mlp sel
Map values for surface "PheA:GrsA_Phe_AMP_1amu.pdb_A SES surface": minimum
-27.37, mean -4.714, maximum 25.54
To also show corresponding color key, enter the above mlp command and add key
true
> color bfactor sel
4281 atoms, 805 residues, 1 surfaces, atom bfactor range 11.6 to 90.3
> mlp sel
Map values for surface "PheA:GrsA_Phe_AMP_1amu.pdb_A SES surface": minimum
-27.37, mean -4.714, maximum 25.54
To also show corresponding color key, enter the above mlp command and add key
true
> undo
[Repeated 9 time(s)]
> surface hidePatches (#!1 & sel)
> select /A
4281 atoms, 4075 bonds, 4 pseudobonds, 805 residues, 3 models selected
> surface hidePatches (#!1 & sel)
> show sel surfaces
> hide sel surfaces
> mlp sel
Map values for surface "PheA:GrsA_Phe_AMP_1amu.pdb_A SES surface": minimum
-27.37, mean -4.714, maximum 25.54
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> surface style solid
> mlp sel
Map values for surface "PheA:GrsA_Phe_AMP_1amu.pdb_A SES surface": minimum
-27.37, mean -4.714, maximum 25.54
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A GLU 34
/A GLU 63
/A GLU 122
/A LYS 125
/A GLU 126
/A ARG 127
/A ASP 133
/A GLN 136
/A ARG 138
/A LYS 144
/A ILE 150
/A HIS 151
/A ASN 152
/A ILE 153
/A GLN 154
/A ASN 156
/A GLU 164
/A ASP 165
/A ILE 167
/A LYS 168
/A ILE 169
/A LYS 180
/A LYS 223
/A LYS 256
/A LYS 264
/A GLU 290
/A GLU 315
/A LYS 316
/A LYS 339
/A GLU 340
/A THR 341
/A LYS 434
/A ARG 436
/A ARG 439
/A LYS 464
/A GLU 468
/A LYS 480
/A GLU 485
/A LYS 521
/A ASP 527
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/7j/5nr95ws55bbf8ytlrz5h2fqw0000gn/T/tmpsh4fubvs/ante.in.mol2 -fi
mol2 -o
/var/folders/7j/5nr95ws55bbf8ytlrz5h2fqw0000gn/T/tmpsh4fubvs/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/7j/5nr95ws55bbf8ytlrz5h2fqw0000gn/T/tmpsh4fubvs/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 29
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 49
| QMMM: diag iterations used for timing = 20
| QMMM:
| QMMM: Internal diag routine = 0.004751 seconds
| QMMM: Dspev diag routine = 0.005407 seconds
| QMMM: Dspevd diag routine = 0.004660 seconds
| QMMM: Dspevx diag routine = 0.020048 seconds
| QMMM: Dsyev diag routine = 0.005807 seconds
| QMMM: Dsyevd diag routine = 0.005244 seconds
| QMMM: Dsyevr diag routine = 0.005959 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.001008 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 N 36.3810 127.0640 21.2220
QMMM: 2 2 C 36.5880 127.8390 19.9910
QMMM: 3 3 C 37.1110 126.9780 18.8320
QMMM: 4 4 O 37.4710 127.4970 17.7730
QMMM: 5 5 C 37.5450 129.0090 20.2440
QMMM: 6 6 H 36.9870 127.2270 22.0140
QMMM: 7 7 H 35.6260 128.2540 19.6910
QMMM: 8 8 C 35.4140 126.1520 21.3210
QMMM: 9 9 C 35.2970 125.3850 22.6410
QMMM: 10 10 H 35.2230 126.0990 23.4750
QMMM: 11 11 H 34.3970 124.7530 22.6190
QMMM: 12 12 H 36.1860 124.7520 22.7770
QMMM: 13 13 N 37.1470 125.6650 19.0400
QMMM: 14 14 C 37.6070 124.7180 18.0280
QMMM: 15 15 H 38.0010 125.2690 17.1610
QMMM: 16 16 H 36.7660 124.0860 17.7080
QMMM: 17 17 H 38.4010 124.0850 18.4520
QMMM: 18 18 H 36.8440 125.3080 19.9350
QMMM: 19 19 O 34.6470 125.8980 20.3910
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1998E+06 DeltaE = -0.4948E-07 DeltaP = 0.1124E-04
QMMM: Smallest DeltaE = -0.4948E-07 DeltaP = 0.1124E-04 Step = 1000
Failure running ANTECHAMBER for residue HIS Check reply log for details
> color sel bychain
> color sel byhetero
> color sel bynucleotide
> hide sel surfaces
> surface hidePatches (#!1 & sel)
> color (#!1 & sel) dark gray
> color (#!1 & sel) cornflower blue
> color (#!1 & sel) byelement
> color (#!1 & sel) light gray
> color (#!1 & sel) byelement
> set bgColor white
> set bgColor gray
> set bgColor white
> set bgColor black
> view sel
> select /B
4267 atoms, 4074 bonds, 5 pseudobonds, 789 residues, 3 models selected
> hide sel cartoons
> select /A
4281 atoms, 4075 bonds, 4 pseudobonds, 805 residues, 3 models selected
> select clear
> select ::name="AMP"
46 atoms, 50 bonds, 2 residues, 1 model selected
> color sel yellow
> color sel byelement
No visible Surface models selected
> color sel byhetero
> color sel orange
> color sel byhetero
> color sel cornflower blue
> color sel byhetero
> select ::name="PHE"
442 atoms, 444 bonds, 40 residues, 1 model selected
> select ligand
80 atoms, 82 bonds, 6 residues, 1 model selected
> color sel cyan
> color sel byhetero
> select ::name="AMP"
46 atoms, 50 bonds, 2 residues, 1 model selected
> color sel cornflower blue
> color sel byhetero
> select /A:126
5 atoms, 4 bonds, 1 residue, 1 model selected
Drag select of 5 atoms, 219 residues, 5 bonds
Drag select of 41 residues
Drag select of 5 residues
> desel
Unknown command: desel
> deselect
Unknown command: deselect
> info selection
atom id /A:361@N idatm_type Npl
atom id /A:361@CA idatm_type C3
atom id /A:361@C idatm_type C2
atom id /A:361@O idatm_type O2
atom id /A:361@CB idatm_type C3
atom id /A:361@CG idatm_type Cac
atom id /A:361@OD1 idatm_type O2-
atom id /A:361@OD2 idatm_type O2-
atom id /A:362@N idatm_type Npl
atom id /A:362@CA idatm_type C3
atom id /A:362@C idatm_type C2
atom id /A:362@O idatm_type O2
atom id /A:362@CB idatm_type C3
atom id /A:362@CG idatm_type C3
atom id /A:362@CD idatm_type Cac
atom id /A:362@OE1 idatm_type O2-
atom id /A:362@OE2 idatm_type O2-
atom id /A:363@N idatm_type Npl
atom id /A:363@CA idatm_type C3
atom id /A:363@C idatm_type C2
atom id /A:363@O idatm_type O2
atom id /A:363@CB idatm_type C3
atom id /A:363@CG idatm_type C2
atom id /A:363@OD1 idatm_type O2
atom id /A:363@ND2 idatm_type Npl
atom id /A:365@N idatm_type Npl
atom id /A:365@CA idatm_type C3
atom id /A:365@C idatm_type C2
atom id /A:365@O idatm_type O2
atom id /A:365@CB idatm_type C3
atom id /A:365@CG idatm_type C3
atom id /A:365@CD idatm_type C2
atom id /A:365@OE1 idatm_type O2
atom id /A:365@NE2 idatm_type Npl
atom id /A:366@N idatm_type Npl
atom id /A:366@CA idatm_type C3
atom id /A:366@C idatm_type C2
atom id /A:366@O idatm_type O2
atom id /A:366@CB idatm_type C3
atom id /A:366@CG idatm_type C3
atom id /A:366@CD1 idatm_type C3
atom id /A:366@CD2 idatm_type C3
Drag select of 1 residues
> info selection
atom id /A:388@N idatm_type Npl
atom id /A:388@CA idatm_type C3
atom id /A:388@C idatm_type C2
atom id /A:388@O idatm_type O2
atom id /A:388@CB idatm_type C3
atom id /A:388@CG idatm_type C3
atom id /A:388@CD idatm_type C3
atom id /A:388@CE idatm_type C3
atom id /A:388@NZ idatm_type N3+
> name frozen
Missing or invalid "name" argument: Expected a text string
Drag select of 33 atoms, 260 residues, 1 pseudobonds, 33 bonds
Drag select of 2 atoms, 192 residues, 2 bonds
Drag select of 39 residues
Drag select of 22 residues
Drag select of 18 residues
Drag select of 16 residues
Drag select of 26 residues
Drag select of 44 residues
[Repeated 1 time(s)]Drag select of 7 residues
Drag select of 5 atoms, 7 residues, 4 bonds
Drag select of 26 residues
Drag select of 5 atoms, 13 residues, 4 bonds
Drag select of 2 residues
Drag select of 23 residues
Drag select of 5 atoms, 14 residues, 4 bonds
Drag select of 22 residues
Drag select of 45 residues
Drag select of 24 residues
Drag select of 5 atoms, 18 residues, 4 bonds
Drag select of 2 atoms, 7 residues, 1 bonds
Drag select of 5 atoms, 36 residues, 4 bonds
Drag select of 40 atoms, 333 residues, 1 pseudobonds, 41 bonds
Drag select of 5 atoms, 4 residues, 4 bonds
Drag select of 4 residues
Drag select of 6 residues
Drag select of 31 residues
Drag select of 40 atoms, 509 residues, 1 pseudobonds, 41 bonds
Drag select of 4 residues
Drag select of 7 residues
Drag select of 14 residues
Drag select of 11 residues
Drag select of 5 residues
Drag select of 8 residues
[Repeated 1 time(s)]Drag select of 7 residues
Drag select of 5 residues
Drag select of 7 residues
Drag select of 3 residues
Drag select of 11 residues
Drag select of 7 residues
Drag select of 13 residues
Drag select of 3 residues
Drag select of 5 atoms, 3 residues, 4 bonds
Drag select of 6 residues
Drag select of 1 residues
Drag select of 9 residues
Drag select of 2 residues
> select clear
> surface
> surface hidePatches
> select main
7897 atoms, 8067 bonds, 3 pseudobonds, 1017 residues, 2 models selected
> select ligand
80 atoms, 82 bonds, 6 residues, 1 model selected
> color sel orange
> color sel byhetero
> color sel yellow
> color sel byhetero
> select ::name="AMP"
46 atoms, 50 bonds, 2 residues, 1 model selected
> color sel cornflower blue
> color sel byhetero
> select clear
> help help:user/menu.html#named-selections
> view
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right select
> select /A:42
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:76
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /A:567@O2'
1 atom, 1 residue, 1 model selected
> select /A:567@C4
1 atom, 1 residue, 1 model selected
> select clear
> select /A:335
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:334
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:336
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:461
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right zoom
> ui mousemode right label
> label #1/A:430
> select clear
> label #1/A:566
> ui mousemode right zoom
> select ::name="ASP"
340 atoms, 298 bonds, 44 residues, 1 model selected
> select clear
> ui mousemode right select
> select /A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select D235
Expected an objects specifier or a keyword
> select 235
Expected an objects specifier or a keyword
> select Asp235
Expected an objects specifier or a keyword
> select 235
Expected an objects specifier or a keyword
> help help:user
> select
8548 atoms, 8149 bonds, 9 pseudobonds, 1594 residues, 3 models selected
> select 235
Expected an objects specifier or a keyword
> select residues 235
Invalid "residues" argument: Expected true or false (or 1 or 0)
> select
8548 atoms, 8149 bonds, 9 pseudobonds, 1594 residues, 3 models selected
> select residues true
8548 atoms, 8149 bonds, 9 pseudobonds, 1594 residues, 3 models selected
> select clear
> select residues true
8548 atoms, 8149 bonds, 9 pseudobonds, 1594 residues, 3 models selected
> select residues flase
Invalid "residues" argument: Expected true or false (or 1 or 0)
> select residues false
8548 atoms, 8149 bonds, 9 pseudobonds, 1594 residues, 3 models selected
> select ::name="MG"
2 atoms, 2 residues, 1 model selected
> show sel atoms
> select residues
Missing "residues" keyword's argument
> select residues
Missing "residues" keyword's argument
> select /A:460
7 atoms, 6 bonds, 1 residue, 1 model selected
> select residues
Missing "residues" keyword's argument
> select clear
> select residues 235 true
Invalid "residues" argument: Expected true or false (or 1 or 0)
> select [residue 235]
Expected an objects specifier or a keyword
> select [residue 235 true]
Expected an objects specifier or a keyword
> select /A ASP235
Expected a keyword
> select A ASP235
Expected an objects specifier or a keyword
> select A 235
Expected an objects specifier or a keyword
> /A:235
Unknown command: /A:235
> select /A:235
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right zoom
> show sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> color (#!1 & sel) white
> color (#!1 & sel) byhetero
> select /A
4281 atoms, 4075 bonds, 4 pseudobonds, 805 residues, 3 models selected
> select clear
> select /A:235
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> style sel sphere
Changed 8 atom styles
> style sel ball
Changed 8 atom styles
> hide sel cartoons
> show sel cartoons
> style sel stick
Changed 8 atom styles
> color (#!1 & sel) black
> color (#!1 & sel) white
> set bgColor white
> set bgColor #ffffff00
> color (#!1 & sel) lime
> color (#!1 & sel) byhetero
> select /A:517
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) lime
> color (#!1 & sel) byhetero
> select /A:236
5 atoms, 4 bonds, 1 residue, 1 model selected
> color (#!1 & sel) #ffffffff
> select /A:236
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) lime
> color (#!1 & sel) byhetero
> label (#!1 & sel) attribute label_specifier
> label (#!1 & sel) attribute name
> label (#!1 & sel) attribute label_specifier
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label (#!1 & sel) text Ala236
> select /A:235
8 atoms, 7 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text Asp235
> select /A:517
9 atoms, 8 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text Lys517
> select /A:239
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) lime
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Trp239
> select /A:278
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) lime
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Thr278
> select /A:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) lime
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Ile299
> select /A:301
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) lime
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Ala301
> select /A:322
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) lime
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Ala322
> select /A:330
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) lime
> color (#!1 & sel) byhetero
[Repeated 1 time(s)]
> label (#!1 & sel) text Ile330
> select /A:331
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:331
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) lime
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Cys331
> save /Users/lei_zhong/Desktop/test.cxs
> select clear
> select /A:326
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> show sel atoms
> color (#!1 & sel) magenta
> color (#!1 & sel) byhetero
> color (#!1 & sel) hot pink
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Thr326
> select /A:327
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) hot pink
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Glu327
> select /A:386
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> color (#!1 & sel) hot pink
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Tyr386
> select /A:190
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) hot pink
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Thr190
> select /A:323
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) hot pink
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Tyr323
> select /A:413
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) hot pink
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Asp413
> select /A:425
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) hot pink
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Tyr425
> select /A:347
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) hot pink
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Pro347
> select /A:321
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) hot pink
> color (#!1 & sel) byhetero
> label (#!1 & sel) text Asn321
> save /Users/lei_zhong/Desktop/test.cxs
[Repeated 1 time(s)]
——— End of log from Sat Aug 12 13:34:07 2023 ———
opened ChimeraX session
> select /B:429-530
823 atoms, 843 bonds, 102 residues, 1 model selected
> select /A:429-530
810 atoms, 830 bonds, 102 residues, 1 model selected
> color (#!1 & sel) dark gray
> select /A:17-428
3138 atoms, 3203 bonds, 1 pseudobond, 407 residues, 2 models selected
> color (#!1 & sel) cornflower blue
[Repeated 1 time(s)]
> select clear
> ui mousemode right zoom
Drag select of 5 atoms, 84 residues, 4 bonds
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
Drag select of 7 atoms, 73 residues, 6 bonds
> hide sel cartoons
Drag select of 5 atoms, 4 bonds
> hide sel atoms
Drag select of 74 residues
> hide sel cartoons
Drag select of 69 residues
> hide sel cartoons
> undo
[Repeated 9 time(s)]
> select clear
Drag select of 36 atoms, 1 pseudobonds, 37 bonds
> hide sel atoms
> select /A:17
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 3 time(s)]
> select /A
4281 atoms, 4075 bonds, 4 pseudobonds, 805 residues, 3 models selected
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> undo
[Repeated 2 time(s)]
> select /A:17
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 2 time(s)]
> select /A:17-20
30 atoms, 30 bonds, 4 residues, 1 model selected
> select /A:17-40
196 atoms, 200 bonds, 24 residues, 1 model selected
> hide sel cartoons
> select /A:17
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:40
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:41
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:41-51
95 atoms, 96 bonds, 11 residues, 1 model selected
> select /A:41-81
337 atoms, 342 bonds, 41 residues, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select /A:41-81
337 atoms, 342 bonds, 41 residues, 1 model selected
> hide sel cartoons
> select /A:42
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:82-92
81 atoms, 80 bonds, 11 residues, 1 model selected
> select /A:82-102
157 atoms, 156 bonds, 21 residues, 1 model selected
> select /A:82-122
298 atoms, 300 bonds, 41 residues, 1 model selected
> hide sel cartoons
> select /A:123
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:123-150
211 atoms, 215 bonds, 28 residues, 1 model selected
> select /A:123-170
347 atoms, 353 bonds, 48 residues, 1 model selected
> select /A:123-190
500 atoms, 510 bonds, 68 residues, 1 model selected
> select /A:123-180
420 atoms, 428 bonds, 58 residues, 1 model selected
> hide sel cartoons
> select /A:520-530
89 atoms, 91 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select /A:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
Drag select of 5 atoms, 2 residues, 4 bonds
Drag select of 5 atoms, 4 bonds
> hide sel atoms
> select /A:181-185
34 atoms, 33 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select /A:181-189
73 atoms, 74 bonds, 9 residues, 1 model selected
> hide sel cartoons
> select /A:191
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:191
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:191-234
304 atoms, 308 bonds, 1 pseudobond, 39 residues, 2 models selected
> hide sel cartoons
> select /A:237-238
13 atoms, 12 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select /A:240-277
307 atoms, 311 bonds, 38 residues, 1 model selected
> hide sel cartoons
> select /A:279-298
159 atoms, 163 bonds, 20 residues, 1 model selected
> hide sel cartoons
> select /A:300
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select /A:302-320
143 atoms, 146 bonds, 19 residues, 1 model selected
> hide sel cartoons
> select /A:324-325
11 atoms, 11 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select /A:328-329
14 atoms, 13 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select /A:332-346
104 atoms, 106 bonds, 15 residues, 1 model selected
> hide sel cartoons
> select /A:348-387
300 atoms, 304 bonds, 40 residues, 1 model selected
> hide sel cartoons
> select /A:348-385
274 atoms, 275 bonds, 38 residues, 1 model selected
> hide sel cartoons
> select /A:387-412
217 atoms, 224 bonds, 26 residues, 1 model selected
> hide sel cartoons
> select /A:414-424
90 atoms, 91 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select /A:426-516
719 atoms, 736 bonds, 91 residues, 1 model selected
> hide sel cartoons
> select /A:517-530
114 atoms, 116 bonds, 14 residues, 1 model selected
> hide sel cartoons
> select /A:517
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select ligand
80 atoms, 82 bonds, 6 residues, 1 model selected
> color sel orange
> color sel byhetero
> style sel ball
Changed 80 atom styles
> select ::name="AMP"
46 atoms, 50 bonds, 2 residues, 1 model selected
> color sel forest green
> color sel byhetero
> select clear
> save /Users/lei_zhong/Desktop/A/Lei/AfcQ/ChimeraX/GraS_1amu_Pocket.cxs
> lighting flat
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting soft
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> save /Users/lei_zhong/Desktop/A/Lei/AfcQ/ChimeraX/GraS_1amu_Pocket.cxs
——— End of log from Sat Aug 12 17:31:50 2023 ———
opened ChimeraX session
> set bgColor white
> select /A
4281 atoms, 4075 bonds, 4 pseudobonds, 805 residues, 3 models selected
> surface style #1.3 solid
> set bgColor black
> surface (#!1 & sel)
> set bgColor white
> transparency (#!1 & sel) 80
> transparency (#!1 & sel) 90
[Repeated 1 time(s)]
> surface style #1.3 mesh
> transparency (#!1 & sel) 90
> surface style #1.3 dot
> surface style #1.3 solid
> save /Users/lei_zhong/Desktop/A/Lei/AfcQ/ChimeraX/GraS_1amu_Pocket.cxs
[Repeated 2 time(s)]
——— End of log from Sat Aug 12 17:39:09 2023 ———
opened ChimeraX session
> select /A:17-530
3948 atoms, 4034 bonds, 1 pseudobond, 509 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> show sel cartoons
> open
> "/Users/lei_zhong/Desktop/A/Lei/AfcQ/ChimeraX/GrsA/GrsA_1amu_Phe_AMP_Acore
> and Asub.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 700, in restore
self.reset()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 149, in reset_state
self.clear()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 700, in restore
self.reset()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 149, in reset_state
self.clear()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 465, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 1004, in open
session.restore(stream, path=path, resize_window=resize_window)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 742, in restore
self.reset()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 149, in reset_state
self.clear()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
AttributeError: 'list' object has no attribute 'values'
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: Z15G0008ZD/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8419.41.10
OS Loader Version: 8419.41.10
Software:
System Software Overview:
System Version: macOS 13.0 (22A380)
Kernel Version: Darwin 22.1.0
Time since boot: 3天21小时12分钟
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL S2319HN:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Restore new session in old ChimeraX |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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