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Opened 3 years ago
Closed 3 years ago
#8269 closed defect (fixed)
ISOLDE: closing structure after paused sim: 'AtomicStructure' object has no attribute '_c_pointer_ref'
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-56-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step20-40min.cxs
Opened m6A-Postprocessresamp.mrc as #1.1.1.1, grid size 384,384,384, pixel
1.1, shown at level 0.00514, step 1, values float32
Log from Wed Dec 21 09:29:38 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open M6A-from-Leo-to-Ewe-After6TAchiralityFixing-FINAL-new.pdb
Chain information for M6A-from-Leo-to-Ewe-After6TAchiralityFixing-FINAL-
new.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
A | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
i | No description available
j | No description available
k | No description available
l | No description available
n | No description available
> hide
> ribbon
> set bgColor white
> open /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/m6A-Postprocessresamp.mrc
Opened m6A-Postprocessresamp.mrc as #2, grid size 384,384,384, pixel 1.1,
shown at level 0.0104, step 2, values float32
> clipper associate #2 toModel #1
Opened m6A-Postprocessresamp.mrc as #1.1.1.1, grid size 384,384,384, pixel
1.1, shown at level 0.0285, step 1, values float32
Chain information for M6A-from-Leo-to-Ewe-After6TAchiralityFixing-FINAL-
new.pdb
---
Chain | Description
1.2/1 | No description available
1.2/2 | No description available
1.2/3 | No description available
1.2/A | No description available
1.2/C | No description available
1.2/D | No description available
1.2/E | No description available
1.2/F | No description available
1.2/G | No description available
1.2/H | No description available
1.2/I | No description available
1.2/J | No description available
1.2/K | No description available
1.2/L | No description available
1.2/M | No description available
1.2/N | No description available
1.2/O | No description available
1.2/P | No description available
1.2/Q | No description available
1.2/R | No description available
1.2/S | No description available
1.2/T | No description available
1.2/U | No description available
1.2/V | No description available
1.2/W | No description available
1.2/X | No description available
1.2/Y | No description available
1.2/Z | No description available
1.2/a | No description available
1.2/b | No description available
1.2/c | No description available
1.2/d | No description available
1.2/e | No description available
1.2/f | No description available
1.2/g | No description available
1.2/i | No description available
1.2/j | No description available
1.2/k | No description available
1.2/l | No description available
1.2/n | No description available
> view #1/5
Drag select of 4 atoms, 2 bonds
> select clear
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> select clear
> addh
Summary of feedback from adding hydrogens to M6A-from-Leo-to-Ewe-
After6TAchiralityFixing-FINAL-new.pdb #1.2
---
warnings | Not adding hydrogens to /3 A 47 P because it is missing heavy-atom
bond partners
Unknown hybridization for atom (P) of residue type 13P; not adding hydrogens
to it
notes | No usable SEQRES records for M6A-from-Leo-to-Ewe-
After6TAchiralityFixing-FINAL-new.pdb (#1.2) chain 1; guessing termini instead
No usable SEQRES records for M6A-from-Leo-to-Ewe-After6TAchiralityFixing-
FINAL-new.pdb (#1.2) chain 2; guessing termini instead
No usable SEQRES records for M6A-from-Leo-to-Ewe-After6TAchiralityFixing-
FINAL-new.pdb (#1.2) chain 3; guessing termini instead
No usable SEQRES records for M6A-from-Leo-to-Ewe-After6TAchiralityFixing-
FINAL-new.pdb (#1.2) chain A; guessing termini instead
No usable SEQRES records for M6A-from-Leo-to-Ewe-After6TAchiralityFixing-
FINAL-new.pdb (#1.2) chain C; guessing termini instead
35 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A CYS 6, /C GLY 3, /D LYS
19, /E GLY 30, /F MET 1, /G MET 1, /H THR 29, /I MET 1, /J SER 5, /K GLY 2, /L
MET 1, /M MET 1, /N MET 1, /O GLY 9, /P GLY 2, /Q SER 16, /R VAL 4, /S PRO 6,
/T MET 1, /U PRO 6, /V VAL 4, /W ALA 16, /X MET 1, /Y VAL 2, /Z MET 1, /a ASP
3, /b THR 2, /c MET 1, /d ARG 5, /e GLN 4, /f LYS 82, /g THR 2, /i VAL 76, /j
GLY 8, /k LYS 4, /l MET 1, /n ARG 41
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /C GLU 209, /G GLY 263, /H ARG
219, /I LEU 237, /J LEU 194, /K GLY 207, /L GLY 188, /M ARG 98, /N PHE 158, /O
LYS 132, /P ALA 151, /Q LEU 151, /S ARG 146, /V LYS 144, /W ALA 119, /Y PHE
130, /c HIS 84, /f LYS 152, /g ILE 314, /i SER 133, /j ILE 115, /k ASP 598, /l
LYS 25
Chain-final residues that are not actual C termini: /A VAL 271, /D GLY 233, /E
THR 255, /F LYS 227, /R PRO 143, /T MET 126, /U LYS 150, /X PHE 83, /Z ARG
142, /a GLY 128, /b ARG 100, /d LEU 68, /e ASP 56, /n GLY 115
7944 hydrogen bonds
/A VAL 271 is not terminus, removing H atom from 'C'
/D GLY 233 is not terminus, removing H atom from 'C'
/E THR 255 is not terminus, removing H atom from 'C'
/F LYS 227 is not terminus, removing H atom from 'C'
/R PRO 143 is not terminus, removing H atom from 'C'
9 messages similar to the above omitted
68998 hydrogens added
> isolde restrain ligands #1
> select clear
[Repeated 1 time(s)]
> view #1/3:49|/A:55|/H:146-147
> isolde restrain ligands #1
> select #1/3:49|/A:55|/H:146-147
77 atoms, 77 bonds, 4 residues, 1 model selected
> isolde sim start sel
Loading residue template for 13P from internal database
ISOLDE: stopped sim
> isolde parameterise sel override true
Running ANTECHAMBER command: /usr/lib/ucsf-
chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmp79sq07ni/ante.in.mol2 -fi mol2 -o /tmp/tmp79sq07ni/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(13P) ``
(13P) `Welcome to antechamber 20.0: molecular input file processor.`
(13P) ``
(13P) `Info: Finished reading file (/tmp/tmp79sq07ni/ante.in.mol2); atoms read
(50), bonds read (51).`
(13P) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(13P) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(13P) ``
(13P) ``
(13P) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(13P) `Info: Total number of electrons: 222; net charge: 0`
(13P) ``
(13P) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`
(13P) ``
(13P) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-
chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`
(13P) ``
(13P) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(13P) ``
Charges for residue 13P determined
OpenMM ffXML file 13P written to the current working directory.
New template added to forcefield as USER_13P. 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.
> view #1/3:49|/A:55|/H:146-147
> select #1/3:49|/A:55|/H:146-147
77 atoms, 77 bonds, 4 residues, 1 model selected
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/3:49|/A:55|/H:146-147
77 atoms, 77 bonds, 4 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/3:49|/A:55|/H:146-147
77 atoms, 77 bonds, 4 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/3:49|/A:55|/H:146-147
77 atoms, 77 bonds, 4 residues, 1 model selected
> isolde sim start sel
> isolde restrain distances
Missing or invalid "atoms" argument: empty atom specifier
> restrain help
Unknown command: restrain help
> isolde restrain distances #1/A:50-62,#1/H:144-149,#1/3:49
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> select #1/3:49|/A:55|/H:146-147
77 atoms, 77 bonds, 4 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde sim pause
> select clear
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Image-Distance-Restainings-at-beginning-M6A-center.png
> width 3200 height 2117 supersample 3
> isolde sim resume
> select clear
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step0.cxs
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step0.pdb
> select #1/3:49|/A:55|/H:146-147
77 atoms, 77 bonds, 4 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/3:49|/A:55|/H:146-147
77 atoms, 77 bonds, 4 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/3:49|/A:55|/H:146-147
77 atoms, 77 bonds, 4 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step1-2min.pdb
> isolde sim resume
> select clear
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step2-4min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step3-6min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step4-8min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step5-10min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step6-12min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step7-14min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step8-16min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step9-18min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step10-20min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step11-22min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step12-24min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step13-26min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step14-28min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step16-30min.pdb
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step18-32min.pdb
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step17-34min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step18-36min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step19-38min.pdb
> isolde sim resume
> isolde sim pause
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step20-40min.pdb
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step20-40min.cxs
> isolde sim stop
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
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step20-40min.cxs
——— End of log from Wed Dec 21 09:29:38 2022 ———
opened ChimeraX session
> select #1/3:49|/A:55|/H:144-149
138 atoms, 138 bonds, 8 residues, 1 model selected
> view #1/3:49|/A:55|/H:144-149
> select #1/3:49|/A:55|/H:144-149
138 atoms, 138 bonds, 8 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
ISOLDE: created disulfide bonds between the following residues:
b23-b74
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/3:49|/A:55|/H:144-149
138 atoms, 138 bonds, 8 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> view #1/1:38
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/3:49|/A:55|/H:144-149
138 atoms, 138 bonds, 8 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/3:49|/A:55|/H:144-149
138 atoms, 138 bonds, 8 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/3:49|/A:55|/H:144-149
138 atoms, 138 bonds, 8 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/3:49|/A:55|/H:144-149|/1:37
188 atoms, 190 bonds, 9 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/A:52
> select #1/A:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> view #1/A:52
> close
> open /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/M6A-300K-restrainings-Relaxed-step0.pdb
Chain information for M6A-300K-restrainings-Relaxed-step0.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
A | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
i | No description available
j | No description available
k | No description available
l | No description available
n | No description available
> hide
> ribbon
> open /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/m6A-Postprocessresamp.mrc
Opened m6A-Postprocessresamp.mrc as #2, grid size 384,384,384, pixel 1.1,
shown at level 0.0104, step 2, values float32
> clipper associate #2 toModel #1
Opened m6A-Postprocessresamp.mrc as #1.1.1.1, grid size 384,384,384, pixel
1.1, shown at level 0.0285, step 1, values float32
Chain information for M6A-300K-restrainings-Relaxed-step0.pdb
---
Chain | Description
1.2/1 | No description available
1.2/2 | No description available
1.2/3 | No description available
1.2/A | No description available
1.2/C | No description available
1.2/D | No description available
1.2/E | No description available
1.2/F | No description available
1.2/G | No description available
1.2/H | No description available
1.2/I | No description available
1.2/J | No description available
1.2/K | No description available
1.2/L | No description available
1.2/M | No description available
1.2/N | No description available
1.2/O | No description available
1.2/P | No description available
1.2/Q | No description available
1.2/R | No description available
1.2/S | No description available
1.2/T | No description available
1.2/U | No description available
1.2/V | No description available
1.2/W | No description available
1.2/X | No description available
1.2/Y | No description available
1.2/Z | No description available
1.2/a | No description available
1.2/b | No description available
1.2/c | No description available
1.2/d | No description available
1.2/e | No description available
1.2/f | No description available
1.2/g | No description available
1.2/i | No description available
1.2/j | No description available
1.2/k | No description available
1.2/l | No description available
1.2/n | No description available
> view #1/5
> addh
Summary of feedback from adding hydrogens to M6A-300K-restrainings-Relaxed-
step0.pdb #1.2
---
warnings | Not adding hydrogens to /3 A 47 P because it is missing heavy-atom
bond partners
Unknown hybridization for atom (P) of residue type 13P; not adding hydrogens
to it
notes | No usable SEQRES records for M6A-300K-restrainings-Relaxed-step0.pdb
(#1.2) chain 1; guessing termini instead
No usable SEQRES records for M6A-300K-restrainings-Relaxed-step0.pdb (#1.2)
chain 2; guessing termini instead
No usable SEQRES records for M6A-300K-restrainings-Relaxed-step0.pdb (#1.2)
chain 3; guessing termini instead
No usable SEQRES records for M6A-300K-restrainings-Relaxed-step0.pdb (#1.2)
chain A; guessing termini instead
No usable SEQRES records for M6A-300K-restrainings-Relaxed-step0.pdb (#1.2)
chain C; guessing termini instead
35 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A CYS 6, /C GLY 3, /D LYS
19, /E GLY 30, /F MET 1, /G MET 1, /H THR 29, /I MET 1, /J SER 5, /K GLY 2, /L
MET 1, /M MET 1, /N MET 1, /O GLY 9, /P GLY 2, /Q SER 16, /R VAL 4, /S PRO 6,
/T MET 1, /U PRO 6, /V VAL 4, /W ALA 16, /X MET 1, /Y VAL 2, /Z MET 1, /a ASP
3, /b THR 2, /c MET 1, /d ARG 5, /e GLN 4, /f LYS 82, /g THR 2, /i VAL 76, /j
GLY 8, /k LYS 4, /l MET 1, /n ARG 41
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /C GLU 209, /G GLY 263, /H ARG
219, /I LEU 237, /J LEU 194, /K GLY 207, /L GLY 188, /M ARG 98, /N PHE 158, /O
LYS 132, /P ALA 151, /Q LEU 151, /S ARG 146, /V LYS 144, /W ALA 119, /Y PHE
130, /c HIS 84, /f LYS 152, /g ILE 314, /i SER 133, /j ILE 115, /k ASP 598, /l
LYS 25
Chain-final residues that are not actual C termini: /A VAL 271, /D GLY 233, /E
THR 255, /F LYS 227, /R PRO 143, /T MET 126, /U LYS 150, /X PHE 83, /Z ARG
142, /a GLY 128, /b ARG 100, /d LEU 68, /e ASP 56, /n GLY 115
7355 hydrogen bonds
/A VAL 271 is not terminus, removing H atom from 'C'
/D GLY 233 is not terminus, removing H atom from 'C'
/E THR 255 is not terminus, removing H atom from 'C'
/F LYS 227 is not terminus, removing H atom from 'C'
/R PRO 143 is not terminus, removing H atom from 'C'
9 messages similar to the above omitted
2 hydrogens added
> isolde restrain ligands #1
> select #1/5
50 atoms, 51 bonds, 1 residue, 1 model selected
> isolde sim start sel
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> view #1/A:55|/3:49|/H:144-149
> view #1/A:55|/3:49|/H:144-149|/1:37
> select #1/A:55|/3:49|/H:144-149|/1:37
188 atoms, 190 bonds, 9 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> isolde restrain distances #1/A:55,#1/H:146-147,#1/3:49
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-
> Asl55_Hsl146-147_3sl49_interface/M6A_m6a-center-Restraining-only-
> eIF2a-uS7-minus3site-interface.jpg width 1265 height 820 supersample 3
> select #1/A:55|/3:49|/H:144-149|/1:37
188 atoms, 190 bonds, 9 residues, 1 model selected
> select clear
> select #1/A:55|/3:49|/H:144-149|/1:37
188 atoms, 190 bonds, 9 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/A:55|/3:49|/H:144-149|/1:37
188 atoms, 190 bonds, 9 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/A:55|/3:49|/H:144-149|/1:37
188 atoms, 190 bonds, 9 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> view #1/5
> view #1/A:55|/3:49|/H:144-149|/1:37
> ui tool show "Ramachandran Plot"
> isolde sim pause
> isolde sim stop
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
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step0.cxs"
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step0.pdb"
> select #1/A:55|/3:49|/H:144-149|/1:37
188 atoms, 190 bonds, 9 residues, 1 model selected
> select #1/A:55|/3:49|/H:144-149|/1:37
188 atoms, 190 bonds, 9 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> view #1/5
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/A:55|/3:49|/H:144-149|/1:37
> select #1/A:55|/3:49|/H:144-149|/1:37
188 atoms, 190 bonds, 9 residues, 1 model selected
> select #1/A:55|/3:49|/H:144-149|/1:37
188 atoms, 190 bonds, 9 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step1-2min.pdb"
> isolde sim resume
> isolde sim pause
[Repeated 1 time(s)]
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step2-4min.pdb"
> isolde sim resume
> view #1/1:35|/3:53
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step3-6min.pdb"
> isolde sim resume
> view #1/A:55|/3:49|/H:144-149|/1:37
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step4-8min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step5-10min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step6-12min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step7-14min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step8-16min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step9-18min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step10-20min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step11-22min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step12-24min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step13-26min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step14-28min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step15-30min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step16-32min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step17-34min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step18-36min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step19-38min.pdb"
> isolde sim resume
> isolde sim pause
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step20-40min.pdb"
> save "/srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A/Post-Phenix-Refinement/After-Correction-4sulfide-
> bond-chain-e/with-all-nucleot-modifications/send-by-
> Ewe-14-11-2022/Correcting-the-Butyl-to-propyl-group-in-13P/after-we-
> discovery-theChirality-errorOn6TA-usingPoseII/MD-experiments-in-ISOLDE-
> probing-stability/M6A_M6A-center-300K/Restraining-Distances-around-A-H-
> mRNA-49site-contacts/Restraining-only-Asl55_Hsl146-147_3sl49_interface/
> M6A_m6aCenter_300K-MD_RestrainingOnlyInterface-step20-40min.cxs"
> close
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/position.py", line 118, in
_selection_changed_cb
sel = self.isolde.selected_atoms
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/distance.py", line 150, in
_selection_changed_cb
sel = self.isolde.selected_atoms
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/secondary_structure.py", line 79,
in _selection_changed_cb
sel = self.isolde.selected_atoms.unique_residues
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/register_shift.py", line 105, in
_selection_changed_cb
sel = self.isolde.selected_atoms
File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 445, in selected_atoms
return m.atoms[m.atoms.selecteds]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
Error processing trigger "selection changed":
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 470.141.03
OpenGL renderer: Quadro K4200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision Tower 5810
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v3 @ 3.50GHz
Cache Size: 15360 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 9.2Gi 12Gi 152Mi 9.2Gi 21Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK104GL [Quadro K4200] [10de:11b4] (rev a1)
Subsystem: NVIDIA Corporation GK104GL [Quadro K4200] [10de:1096]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
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: 2.2.4
ChimeraX-Clipper: 0.18.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
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: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
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: 1.4
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
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: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
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: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
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: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
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: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
distro: 1.6.0
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE: closing structure after paused sim: 'AtomicStructure' object has no attribute '_c_pointer_ref' |
comment:2 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Reported by Leonardo Lima