Opened 3 years ago

Closed 3 years ago

#8280 closed defect (fixed)

ISOLDE: 'close' after 'sim pause': 'AtomicStructure' object has no attribute '_c_pointer_ref'

Reported by: leofrancalima@… 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-5.15.0-57-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 M6A-P_m6aCenter_300K-MD_RestrainingOnlyInterface-step0.cxs

Opened m6APKR-postprocess34Resampled.mrc as #1.1.1.1, grid size 384,384,384,
pixel 1.1, shown at level 0.0272, step 1, values float32  
Log from Fri Jan 6 09:57:40 2023UCSF 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-P_300K-MD_m6a-center_Snps-0.pdb

Chain information for M6A-P_300K-MD_m6a-center_Snps-0.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+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/m6APKR-postprocess34Resampled.mrc

Opened m6APKR-postprocess34Resampled.mrc as #2, grid size 384,384,384, pixel
1.1, shown at level 0.0129, step 2, values float32  

> clipper associate #2 toModel #1

Opened m6APKR-postprocess34Resampled.mrc as #1.1.1.1, grid size 384,384,384,
pixel 1.1, shown at level 0.0272, step 1, values float32  
Chain information for M6A-P_300K-MD_m6a-center_Snps-0.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

> isolde start

> set selectionWidth 4

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

> addh

Summary of feedback from adding hydrogens to
M6A-P_300K-MD_m6a-center_Snps-0.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-P_300K-MD_m6a-center_Snps-0.pdb
(#1.2) chain 1; guessing termini instead  
No usable SEQRES records for M6A-P_300K-MD_m6a-center_Snps-0.pdb (#1.2) chain
2; guessing termini instead  
No usable SEQRES records for M6A-P_300K-MD_m6a-center_Snps-0.pdb (#1.2) chain
3; guessing termini instead  
No usable SEQRES records for M6A-P_300K-MD_m6a-center_Snps-0.pdb (#1.2) chain
A; guessing termini instead  
No usable SEQRES records for M6A-P_300K-MD_m6a-center_Snps-0.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: /I THR 171, /I ARG 178,
/Z TYR 27  
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, /I PRO 169, /I ILE 176, /R PRO 143, /T MET 126, /U LYS
150, /X PHE 83, /Z ARG 142, /Z LYS 25, /a GLY 128, /b ARG 100, /d LEU 68, /e
ASP 56, /n GLY 115  
6900 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  
0 hydrogens added  
  

> isolde restrain ligands #1

> select clear

[Repeated 3 time(s)]

> view #1/A:55|/H:144-149|/3:49|/1:37

> select #1/A:55|/H:144-149|/3:49|/1:37

188 atoms, 190 bonds, 9 residues, 1 model selected  

> 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+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-the-m6a-eIF2a-uS7-interfaces/M6A-P-restrainings-
> Only-m6aCenter-interfaces.jpg width 1265 height 837 supersample 3

> select #1/A:55|/H:144-149|/3:49|/1:37

188 atoms, 190 bonds, 9 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/tmpbj23kbei/ante.in.mol2 -fi mol2 -o /tmp/tmpbj23kbei/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/tmpbj23kbei/ante.in.mol2); atoms read
(49), bonds read (50).`  
(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: 214; 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.  

> select #1/A:55|/H:144-149|/3:49|/1:37

188 atoms, 190 bonds, 9 residues, 1 model selected  

> view #1/A:55|/H:144-149|/3:49|/1:37

> select #1/A:55|/H:144-149|/3:49|/1:37

188 atoms, 190 bonds, 9 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  

> view #1/5

> view #1/A:55|/H:144-149|/3:49|/1:37

> 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|/H:144-149|/3:49|/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|/H:144-149|/3:49|/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/A:52

> view #1/A:61

> view #1/A:52

> view #1/A:55|/H:144-149|/3:49|/1:37

> select clear

> select #1/A:55|/H:144-149|/3:49|/1:37

188 atoms, 190 bonds, 9 residues, 1 model selected  

> view #1/5

> view #1/A:55|/H:144-149|/3:49|/1:37

> 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+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/M6A-P_m6aCenter_300K-MD_RestrainingOnlyInterface-
> step0.cxs

——— End of log from Fri Jan 6 09:57:40 2023 ———

opened ChimeraX session  

> isolde start

> set selectionWidth 4

> select clear

> view #1/5

> addh

Summary of feedback from adding hydrogens to
M6A-P_300K-MD_m6a-center_Snps-0.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-P_300K-MD_m6a-center_Snps-0.pdb
(#1.2) chain 1; guessing termini instead  
No usable SEQRES records for M6A-P_300K-MD_m6a-center_Snps-0.pdb (#1.2) chain
2; guessing termini instead  
No usable SEQRES records for M6A-P_300K-MD_m6a-center_Snps-0.pdb (#1.2) chain
3; guessing termini instead  
No usable SEQRES records for M6A-P_300K-MD_m6a-center_Snps-0.pdb (#1.2) chain
A; guessing termini instead  
No usable SEQRES records for M6A-P_300K-MD_m6a-center_Snps-0.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: /I THR 171, /I ARG 178,
/Z TYR 27  
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, /I PRO 169, /I ILE 176, /R PRO 143, /T MET 126, /U LYS
150, /X PHE 83, /Z ARG 142, /Z LYS 25, /a GLY 128, /b ARG 100, /d LEU 68, /e
ASP 56, /n GLY 115  
6903 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  
0 hydrogens added  
  

> isolde restrain ligands #1

> 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  

> 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/tmpvw46j12q/ante.in.mol2 -fi mol2 -o /tmp/tmpvw46j12q/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/tmpvw46j12q/ante.in.mol2); atoms read
(49), bonds read (50).`  
(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: 214; 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/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  

> 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/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 pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step1-2min.pdb

> isolde sim resume

> ui tool show "Ramachandran Plot"

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step2-4min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step3-6min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step4-8min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step5-10min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step6-12min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step7-14min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step8-16min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step9-18min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step10-20min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step11-22min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step12-24min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step13-26min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step14-28min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step15-30min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step16-32min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step17-34min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step18-36min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step19-38min.pdb

> isolde sim resume

> isolde sim pause

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-step20-40min.pdb

> save /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/m6A+phosphorylation/Refinement-from-
> step3-withoutAddingPhosphate/Post-Phenix/After-correction-4sulfideBond-
> chain-e/with-all-nucleot-modifications/Sent-By-Ewe-
> with-M6A-in-14-11-2022/Final-system-with-explicit-6TA-
> and-13P/Refining-13P-group/Step-2/after-we-discovery-theChirality-
> errorOn6TA/MD-Simulations-Stability/Restraining-the-M6A-center-
> distances/Restraining-Only-
> the-m6a-eIF2a-uS7-interfaces/Sim3/M6A-P_m6aCenter_300K-MD_Sim3-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 470.161.03
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       5.1Gi        18Gi        67Mi       7.5Gi        25Gi
	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 (3)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: 'close' after 'sim pause': 'AtomicStructure' object has no attribute '_c_pointer_ref'

Reported by Leonardo Lima

comment:2 by Tristan Croll, 3 years ago

This is a long-standing limitation that I guess I need to bite the bullet and address: running an interactive simulation involves a lot of quite intricate choreography in the code, and gracefully unravelling all the callbacks when the underlying model suddenly ceases to exist is a bit of a painful task. For now, just make sure you hit stop on any running simulation before closing the model.

comment:3 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

OK, ISOLDE now recovers gracefully if the working model is deleted while a simulation is running (or paused). Fix will be in the next release.

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