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#3281 closed defect (fixed)

Garbled PostiveIntArg error message

Reported by:	Tristan Croll	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Command Line	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 1.0 (2020-05-09)
Description
Error message for an incorrect PositiveIntArg is a bit garbled.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 1.0rc202005090702 (2020-05-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open gprc-dlh1-car.cif

Summary of feedback from opening gprc-dlh1-car.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 225  
Missing entity information. Treating each chain as a separate entity.  
Atom H1 is not in the residue template for MET #1 in chain ba  
Atom C1 is not in the residue template for GPC #101 in chain ba  
Atom H1 is not in the residue template for MET #1 in chain ab  
Atom H1 is not in the residue template for MET #1 in chain bb  
Atom C1 is not in the residue template for GPC #101 in chain bb  
Atom H1 is not in the residue template for MET #1 in chain ac  
Atom H1 is not in the residue template for MET #1 in chain bc  
Atom C1 is not in the residue template for GPC #101 in chain bc  
Atom H1 is not in the residue template for MET #1 in chain ad  
Atom H1 is not in the residue template for MET #1 in chain bd  
Atom C1 is not in the residue template for GPC #101 in chain bd  
Atom H1 is not in the residue template for MET #1 in chain ae  
Atom H1 is not in the residue template for MET #1 in chain be  
Atom C1 is not in the residue template for GPC #101 in chain be  
Atom H1 is not in the residue template for MET #1 in chain af  
Atom H1 is not in the residue template for MET #1 in chain bf  
Atom C1 is not in the residue template for GPC #101 in chain bf  
Atom H1 is not in the residue template for MET #1 in chain ag  
Atom H1 is not in the residue template for MET #1 in chain bg  
Atom C1 is not in the residue template for GPC #101 in chain bg  
Atom H1 is not in the residue template for MET #1 in chain ah  
Atom H1 is not in the residue template for MET #1 in chain bh  
Atom C1 is not in the residue template for GPC #101 in chain bh  
Atom H1 is not in the residue template for MET #1 in chain ai  
Atom H1 is not in the residue template for MET #1 in chain bi  
Atom H1 is not in the residue template for MET #1 in chain aj  
Atom C1 is not in the residue template for GPC #101 in chain aj  
Atom H1 is not in the residue template for MET #1 in chain bj  
Atom C1 is not in the residue template for GPC #101 in chain bj  
Atom H1 is not in the residue template for MET #1 in chain ak  
Atom H1 is not in the residue template for MET #1 in chain bk  
Atom C1 is not in the residue template for GPC #101 in chain bk  
Atom H1 is not in the residue template for MET #1 in chain al  
Atom H1 is not in the residue template for MET #1 in chain bl  
Atom C1 is not in the residue template for GPC #101 in chain bl  
Atom H1 is not in the residue template for MET #1 in chain am  
Atom H1 is not in the residue template for MET #1 in chain bm  
Atom H1 is not in the residue template for MET #1 in chain an  
Atom C1 is not in the residue template for GPC #101 in chain an  
Atom H1 is not in the residue template for MET #1 in chain bn  
Atom C1 is not in the residue template for GPC #101 in chain bn  
Atom H1 is not in the residue template for MET #1 in chain ao  
Atom H1 is not in the residue template for MET #1 in chain bo  
Atom C1 is not in the residue template for GPC #101 in chain bo  
Atom H1 is not in the residue template for MET #1 in chain ap  
Atom H1 is not in the residue template for MET #1 in chain bp  
Atom C1 is not in the residue template for GPC #101 in chain bp  
Atom H1 is not in the residue template for ALA #1 in chain L  
Atom C1 is not in the residue template for GP1 #701 in chain M  
Atom H1 is not in the residue template for SER #1 in chain H2  
Atom H1 is not in the residue template for MET #1 in chain H1  
Atom CH1 is not in the residue template for TRP #47 in chain H1  
Atom H1 is not in the residue template for MET #3 in chain AA  
Atom H1 is not in the residue template for MET #1 in chain BA  
Atom C1 is not in the residue template for GPC #101 in chain BA  
Atom H1 is not in the residue template for MET #3 in chain AW  
Atom H1 is not in the residue template for MET #1 in chain BW  
Atom C1 is not in the residue template for GPC #101 in chain BW  
Atom H1 is not in the residue template for MET #3 in chain AX  
Atom H1 is not in the residue template for MET #1 in chain BX  
Atom C1 is not in the residue template for GPC #101 in chain BX  
Atom H1 is not in the residue template for MET #3 in chain AV  
Atom C1 is not in the residue template for GPC #101 in chain AV  
Atom H1 is not in the residue template for MET #1 in chain BV  
Atom H1 is not in the residue template for MET #3 in chain AU  
Atom H1 is not in the residue template for MET #1 in chain BU  
Atom C1 is not in the residue template for GPC #101 in chain BU  
Atom H1 is not in the residue template for MET #3 in chain AB  
Atom H1 is not in the residue template for MET #1 in chain BB  
Atom C1 is not in the residue template for GPC #101 in chain BB  
Atom H1 is not in the residue template for MET #3 in chain AC  
Atom H1 is not in the residue template for MET #1 in chain BC  
Atom C1 is not in the residue template for GPC #101 in chain BC  
Atom H1 is not in the residue template for MET #3 in chain AD  
Atom H1 is not in the residue template for MET #1 in chain BD  
Atom C1 is not in the residue template for GPC #101 in chain BD  
Atom H1 is not in the residue template for MET #3 in chain AE  
Atom H1 is not in the residue template for MET #1 in chain BE  
Atom C1 is not in the residue template for GPC #101 in chain BE  
Atom H1 is not in the residue template for MET #3 in chain BF  
Atom H1 is not in the residue template for MET #1 in chain AF  
Atom C1 is not in the residue template for GPC #101 in chain AF  
Atom H1 is not in the residue template for MET #3 in chain BG  
Atom H1 is not in the residue template for MET #1 in chain AG  
Atom C1 is not in the residue template for GPC #101 in chain AG  
Atom H1 is not in the residue template for MET #3 in chain AH  
Atom H1 is not in the residue template for MET #1 in chain BH  
Atom C1 is not in the residue template for GPC #101 in chain BH  
Atom H1 is not in the residue template for MET #3 in chain AI  
Atom H1 is not in the residue template for MET #1 in chain BI  
Atom C1 is not in the residue template for GPC #101 in chain BI  
Atom H1 is not in the residue template for MET #3 in chain AJ  
Atom H1 is not in the residue template for MET #1 in chain BJ  
Atom C1 is not in the residue template for GPC #101 in chain BJ  
Atom H1 is not in the residue template for MET #3 in chain AK  
Atom H1 is not in the residue template for MET #1 in chain BK  
Atom C1 is not in the residue template for GPC #101 in chain BK  
Atom H1 is not in the residue template for MET #3 in chain AL  
Atom H1 is not in the residue template for MET #1 in chain BL  
Atom C1 is not in the residue template for GPC #101 in chain BL  
Atom H1 is not in the residue template for MET #3 in chain AM  
Atom H1 is not in the residue template for MET #1 in chain BM  
Atom C1 is not in the residue template for GPC #101 in chain BM  
Atom H1 is not in the residue template for MET #3 in chain AN  
Atom H1 is not in the residue template for MET #1 in chain BN  
Atom C1 is not in the residue template for GPC #101 in chain BN  
Atom H1 is not in the residue template for MET #3 in chain AO  
Atom H1 is not in the residue template for MET #1 in chain BO  
Atom C1 is not in the residue template for GPC #101 in chain BO  
Atom H1 is not in the residue template for MET #3 in chain AP  
Atom H1 is not in the residue template for MET #1 in chain BP  
Atom C1 is not in the residue template for GPC #101 in chain BP  
Atom H1 is not in the residue template for MET #3 in chain AQ  
Atom H1 is not in the residue template for MET #1 in chain BQ  
Atom C1 is not in the residue template for GPC #101 in chain BQ  
Atom H1 is not in the residue template for MET #3 in chain AR  
Atom H1 is not in the residue template for MET #1 in chain BR  
Atom C1 is not in the residue template for GPC #101 in chain BR  
Atom H1 is not in the residue template for MET #3 in chain AS  
Atom H1 is not in the residue template for MET #1 in chain BS  
Atom C1 is not in the residue template for GPC #101 in chain BS  
Atom H1 is not in the residue template for MET #3 in chain AT  
Atom H1 is not in the residue template for MET #1 in chain BT  
Atom C1 is not in the residue template for GPC #101 in chain BT  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 90425  
Skipping chem_comp category: Missing column 'type' near line 90949  
Skipping chem_comp category: Missing column 'type' near line 91841  
Skipping chem_comp category: Missing column 'type' near line 91868  
Skipping chem_comp category: Missing column 'type' near line 92039  
  
Chain information for gprc-dlh1-car.cif #1  
---  
Chain | Description  
AA AB AC AD AE AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX BF BG | No
description available  
AF AG BA BB BC BD BE BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX ba bb
bc bd be bf bg bh bi bj bk bl bm bn bo bp | No description available  
C | No description available  
H1 | No description available  
H2 | No description available  
L | No description available  
M | No description available  
aa | No description available  
ab ac ad ae af ag ah ai aj ak al am an ao ap | No description available  
  

> open
> /run/media/tic20/storage/structure_dump/pu_qian/running/gprclh1-338aleft.mrc

Opened gprclh1-338aleft.mrc, grid size 300,300,300, pixel 1.05, shown at level
0.0201, step 2, values float32  

> clipper associate #2 toModel #1

Chain information for gprc-dlh1-car.cif  
---  
Chain | Description  
1.2/AA 1.2/AB 1.2/AC 1.2/AD 1.2/AE 1.2/AH 1.2/AI 1.2/AJ 1.2/AK 1.2/AL 1.2/AM
1.2/AN 1.2/AO 1.2/AP 1.2/AQ 1.2/AR 1.2/AS 1.2/AT 1.2/AU 1.2/AV 1.2/AW 1.2/AX
1.2/BF 1.2/BG | No description available  
1.2/AF 1.2/AG 1.2/BA 1.2/BB 1.2/BC 1.2/BD 1.2/BE 1.2/BH 1.2/BI 1.2/BJ 1.2/BK
1.2/BL 1.2/BM 1.2/BN 1.2/BO 1.2/BP 1.2/BQ 1.2/BR 1.2/BS 1.2/BT 1.2/BU 1.2/BV
1.2/BW 1.2/BX 1.2/ba 1.2/bb 1.2/bc 1.2/bd 1.2/be 1.2/bf 1.2/bg 1.2/bh 1.2/bi
1.2/bj 1.2/bk 1.2/bl 1.2/bm 1.2/bn 1.2/bo 1.2/bp | No description available  
1.2/C | No description available  
1.2/H1 | No description available  
1.2/H2 | No description available  
1.2/L | No description available  
1.2/M | No description available  
1.2/aa | No description available  
1.2/ab 1.2/ac 1.2/ad 1.2/ae 1.2/af 1.2/ag 1.2/ah 1.2/ai 1.2/aj 1.2/ak 1.2/al
1.2/am 1.2/an 1.2/ao 1.2/ap | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> set bgColor white

> volume gaussian #1 bfactor 50

> clipper associate #2 toModel #1

> select :HEM

292 atoms, 304 bonds, 16 pseudobonds, 2 models selected  

> toolshed show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

2 atoms were automatically renamed to match the template: O1A->O2A, O2A->O1A  

> select up

77 atoms, 84 bonds, 1 model selected  

> style sel stick

Changed 77 atom styles  

> delete sel

> preset custom "make bond"

> open /home/tic20/chimerax_presets/make_bond.py

executed make_bond.py  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> delete sel

> preset custom "make bond"

> open /home/tic20/chimerax_presets/make_bond.py

executed make_bond.py  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

2 atoms were automatically renamed to match the template: O1A->O2A, O2A->O1A  

> select up

77 atoms, 84 bonds, 1 model selected  

> style sel stick

Changed 77 atom styles  

> delete sel

> preset custom "make bond"

> open /home/tic20/chimerax_presets/make_bond.py

executed make_bond.py  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> delete sel

> preset custom "make bond"

> open /home/tic20/chimerax_presets/make_bond.py

executed make_bond.py  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

2 atoms were automatically renamed to match the template: O1A->O2A, O2A->O1A  

> select up

77 atoms, 84 bonds, 1 model selected  

> style sel stick

Changed 77 atom styles  

> delete sel

> preset custom "make bond"

> open /home/tic20/chimerax_presets/make_bond.py

executed make_bond.py  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> delete sel

> preset custom "make bond"

> open /home/tic20/chimerax_presets/make_bond.py

executed make_bond.py  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

2 atoms were automatically renamed to match the template: O1A->O2A, O2A->O1A  

> select up

77 atoms, 84 bonds, 1 model selected  

> style sel stick

Changed 77 atom styles  

> delete sel

> preset custom "make bond"

> open /home/tic20/chimerax_presets/make_bond.py

executed make_bond.py  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> delete sel

> preset custom "make bond"

> open /home/tic20/chimerax_presets/make_bond.py

executed make_bond.py  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> save hec_corrected.cif #1

Not saving entity_poly_seq for non-authoritative sequences  

> select :BCL

11760 atoms, 12096 bonds, 336 pseudobonds, 2 models selected  

> select up

11760 atoms, 12432 bonds, 336 pseudobonds, 2 models selected  

> style sel stick

Changed 11760 atom styles  

> select clear

> save working.cxs

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/symmetry.py", line 1120, in take_snapshot  
from chimerax.core.state import CORE_STATE_VERSION  
ImportError: cannot import name 'CORE_STATE_VERSION' from
'chimerax.core.state' (/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/state.py)  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 817, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 568, in save  
mgr.discovery(self._state_containers)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'custom_attr_preserver' ->
<chimerax.atomic.attr_registration.CustomizedInstanceManager object at
0x7f2eb010e550> -> <chimerax.atomic.molobject.Residue object at
0x7f2df802dfa0> 'GPC' -> <chimerax.atomic.structure.AtomicStructure object at
0x7f2e4c178a10> 'gprc-dlh1-car.cif' ->
<chimerax.clipper.symmetry.SymmetryManager object at 0x7f2eb202a190> 'Data
manager (gprc-dlh1-car.cif)'  
  
RuntimeError: Error while saving session data for 'custom_attr_preserver' ->
-> 'GPC' -> 'gprc-dlh1-car.cif' -> 'Data manager (gprc-dlh1-car.cif)'  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/symmetry.py", line 1120, in take_snapshot  
from chimerax.core.state import CORE_STATE_VERSION  
ImportError: cannot import name 'CORE_STATE_VERSION' from
'chimerax.core.state' (/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/state.py)  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 817, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 568, in save  
mgr.discovery(self._state_containers)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'custom_attr_preserver' ->
<chimerax.atomic.attr_registration.CustomizedInstanceManager object at
0x7f2eb010e550> -> <chimerax.atomic.molobject.Residue object at
0x7f2df802dfa0> 'GPC' -> <chimerax.atomic.structure.AtomicStructure object at
0x7f2e4c178a10> 'gprc-dlh1-car.cif' ->
<chimerax.clipper.symmetry.SymmetryManager object at 0x7f2eb202a190> 'Data
manager (gprc-dlh1-car.cif)'  
  
RuntimeError: Error while saving session data for 'custom_attr_preserver' ->
-> 'GPC' -> 'gprc-dlh1-car.cif' -> 'Data manager (gprc-dlh1-car.cif)'  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 283, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  

> select #1

89256 atoms, 91218 bonds, 354 pseudobonds, 17 models selected  

> delete H

> addh

Summary of feedback from adding hydrogens to gprc-dlh1-car.cif #1.2  
---  
notes | No usable SEQRES records for gprc-dlh1-car.cif (#1.2) chain AA;
guessing termini instead  
No usable SEQRES records for gprc-dlh1-car.cif (#1.2) chain AB; guessing
termini instead  
No usable SEQRES records for gprc-dlh1-car.cif (#1.2) chain AC; guessing
termini instead  
No usable SEQRES records for gprc-dlh1-car.cif (#1.2) chain AD; guessing
termini instead  
No usable SEQRES records for gprc-dlh1-car.cif (#1.2) chain AE; guessing
termini instead  
80 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /AA MET 3, /AB MET 3, /AC
MET 3, /AD MET 3, /AE MET 3, /AF MET 1, /AG MET 1, /AH MET 3, /AI MET 3, /AJ
MET 3, /AK MET 3, /AL MET 3, /AM MET 3, /AN MET 3, /AO MET 3, /AP MET 3, /AQ
MET 3, /AR MET 3, /AS MET 3, /AT MET 3, /AU MET 3, /AV MET 3, /AW MET 3, /AX
MET 3, /BA MET 1, /BB MET 1, /BC MET 1, /BD MET 1, /BE MET 1, /BF MET 3, /BG
MET 3, /BH MET 1, /BI MET 1, /BJ MET 1, /BK MET 1, /BL MET 1, /BM MET 1, /BN
MET 1, /BO MET 1, /BP MET 1, /BQ MET 1, /BR MET 1, /BS MET 1, /BT MET 1, /BU
MET 1, /BV MET 1, /BW MET 1, /BX MET 1, /C ALA 15, /H1 MET 1, /H2 SER 1, /L
ALA 1, /M MET 1, /aa HIS 2, /ab MET 1, /ac MET 1, /ad MET 1, /ae MET 1, /af
MET 1, /ag MET 1, /ah MET 1, /ai MET 1, /aj MET 1, /ak MET 1, /al MET 1, /am
MET 1, /an MET 1, /ao MET 1, /ap MET 1, /ba MET 1, /bb MET 1, /bc MET 1, /bd
MET 1, /be MET 1, /bf MET 1, /bg MET 1, /bh MET 1, /bi MET 1, /bj MET 1, /bk
MET 1, /bl MET 1, /bm MET 1, /bn MET 1, /bo MET 1, /bp MET 1  
Chain-initial residues that are not actual N termini: /H2 ASP 9  
Chain-final residues that are actual C termini: /AF PHE 38, /AG PHE 38, /BA
PHE 38, /BB PHE 38, /BC PHE 38, /BD PHE 38, /BE PHE 38, /BH PHE 38, /BI PHE
38, /BJ PHE 38, /BK PHE 38, /BL PHE 38, /BM PHE 38, /BN PHE 38, /BO PHE 38,
/BP PHE 38, /BQ PHE 38, /BR PHE 38, /BS PHE 38, /BT PHE 38, /BU PHE 38, /BV
PHE 38, /BW PHE 38, /BX PHE 38, /C ARG 302, /H2 ILE 181, /L LYS 273, /ba PHE
38, /bb PHE 38, /bc PHE 38, /bd PHE 38, /be PHE 38, /bf PHE 38, /bg PHE 38,
/bh PHE 38, /bi PHE 38, /bj PHE 38, /bk PHE 38, /bl PHE 38, /bm PHE 38, /bn
PHE 38, /bo PHE 38, /bp PHE 38  
Chain-final residues that are not actual C termini: /AA TYR 43, /AB TYR 43,
/AC TYR 43, /AD TYR 43, /AE TYR 43, /AH TYR 43, /AI TYR 43, /AJ TYR 43, /AK
TYR 43, /AL TYR 43, /AM TYR 43, /AN TYR 43, /AO TYR 43, /AP TYR 43, /AQ TYR
43, /AR TYR 43, /AS TYR 43, /AT TYR 43, /AU TYR 43, /AV TYR 43, /AW TYR 43,
/AX TYR 43, /BF TYR 43, /BG TYR 43, /H1 LYS 53, /H2 PRO 7, /M TYR 324, /aa ALA
60, /ab ALA 60, /ac ALA 60, /ad ALA 60, /ae ALA 60, /af ALA 60, /ag ALA 60,
/ah ALA 60, /ai ALA 60, /aj ALA 60, /ak ALA 60, /al ALA 60, /am ALA 60, /an
ALA 60, /ao ALA 60, /ap ALA 60  
4597 hydrogen bonds  
Adding 'H' to /H2 ASP 9  
/AA TYR 43 is not terminus, removing H atom from 'C'  
/AB TYR 43 is not terminus, removing H atom from 'C'  
/AC TYR 43 is not terminus, removing H atom from 'C'  
/AD TYR 43 is not terminus, removing H atom from 'C'  
/AE TYR 43 is not terminus, removing H atom from 'C'  
38 messages similar to the above omitted  
44863 hydrogens added  
  

> save prep.cif #1

Not saving entity_poly_seq for non-authoritative sequences  

> hide HC

> sequence chain /H1

Alignment identifier is 1.2.H1  

> open 5y5s

5y5s title:  
Structure of photosynthetic LH1-RC super-complex at 1.9 angstrom resolution
[more info...]  
  
Chain information for 5y5s #2  
---  
Chain | Description  
0 2 4 6 8 B E G J N P R T V X Z | LH1 β polypeptide  
1 3 5 7 9 A D F I K O Q S U W Y | LH1 α polypeptide  
C | Photosynthetic reaction center cytochrome c subunit  
H | Photosynthetic reaction center H subunit  
L | Photosynthetic reaction center L subunit  
M | Photosynthetic reaction center M subunit  
  
Non-standard residues in 5y5s #2  
---  
BCL — bacteriochlorophyll A  
BPH — bacteriopheophytin A  
CA — calcium ion  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
CRT — spirilloxanthin (rhodoviolascin)  
FE — Fe (III) ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
HEM — protoporphyrin IX containing Fe (HEME)  
LDA — lauryl dimethylamine-N-oxide  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMT — dodecyl-β-D-maltoside  
MG — magnesium ion  
MQ8 — menaquinone 8 (2-methyl-3-(3,7,11,15,19,23,27,31-octamethyl-
dotriaconta-2,6,10,14,18,22,26,30-octaenyl)-[1,4]napthoquinone)  
PEF — di-palmitoyl-3-Sn-phosphatidylethanolamine
(3-[aminoethylphosphoryl]-[1,2-di-palmitoyl]-Sn-glycerol)  
PGV —
(1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl
(11E)-octadec-11-enoate (phosphatidylglycerol, 2-vaccenoyl-1-palmitoyl-Sn-
glycerol-3-phosphoglycerol)  
SO4 — sulfate ion  
UNL — unknown ligand  
UQ8 — Ubiquinone-8
(2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl]cyclohexa-2,5-diene-1,4-dione)  
  

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker gprc-dlh1-car.cif, chain M (#1.2) with 5y5s, chain M (#2), sequence
alignment score = 1220.4  
RMSD between 293 pruned atom pairs is 0.785 angstroms; (across all 316 pairs:
1.433)  
  

> select #2

27922 atoms, 27717 bonds, 276 pseudobonds, 2 models selected  

> show sel cartoons

> style sel stick

Changed 27922 atom styles  

> select clear

> color #2 byhetero

> select #1/H1

874 atoms, 890 bonds, 1 model selected  

> hide #!2 models

> show sel

> select #1

89295 atoms, 91249 bonds, 354 pseudobonds, 23 models selected  

No template found for residue C501 (HEC)  

Doing nothing  

> show sel

> delete sel

> select up

73 atoms, 80 bonds, 1 model selected  

> select up

4716 atoms, 4814 bonds, 1 model selected  

> select up

89293 atoms, 91247 bonds, 1 model selected  

> select down

4716 atoms, 4814 bonds, 1 model selected  

> select down

73 atoms, 80 bonds, 1 model selected  

No template found for residue C502 (HEC)  

Doing nothing  

> show sel

> delete :HEC@HAC,HAB

> select #1

89287 atoms, 91241 bonds, 354 pseudobonds, 23 models selected  

> select clear

> select clear

> select clear

> select clear

> save working.cif #1

Not saving entity_poly_seq for non-authoritative sequences  

> select ~H

72354 atoms, 118958 bonds, 630 pseudobonds, 25 models selected  

> save working_noh.cif #1 selectedOnly true

Not saving entity_poly_seq for non-authoritative sequences  

> select clear

> select clear

> view /H1:27

> select /H1:27,28,32,44

96 atoms, 93 bonds, 1 model selected  

6 atoms were automatically renamed to match the template: O->OXT, NH1->NH2,
HNH1->HH22, HNH2->HH21, HH11->HH12, HH12->HH11  

6 atoms were automatically renamed to match the template: O->OXT, NH1->NH2,
HH11->HH22, HH12->HH21, HNH1->HH12, HNH2->HH11  

6 atoms were automatically renamed to match the template: O->OXT, NH1->NH2,
HNH1->HH22, HNH2->HH21, HH11->HH12, HH12->HH11  

6 atoms were automatically renamed to match the template: O->OXT, NH1->NH2,
HH11->HH22, HH12->HH21, HNH1->HH12, HNH2->HH11  

> select clear

> save working.cif #1

Not saving entity_poly_seq for non-authoritative sequences  

> sequence chain /H1

Alignment identifier is 1.2.H1  

> open /run/media/tic20/storage/structure_dump/pu_qian/new_2020_05/gprc-
> dlh1-car.cif

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/pu_qian/new_2020_05/gprc-dlh1-car.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 225  
Missing entity information. Treating each chain as a separate entity.  
Atom H1 is not in the residue template for MET #1 in chain ba  
Atom C1 is not in the residue template for GPC #101 in chain ba  
Atom H1 is not in the residue template for MET #1 in chain ab  
Atom H1 is not in the residue template for MET #1 in chain bb  
Atom C1 is not in the residue template for GPC #101 in chain bb  
Atom H1 is not in the residue template for MET #1 in chain ac  
Atom H1 is not in the residue template for MET #1 in chain bc  
Atom C1 is not in the residue template for GPC #101 in chain bc  
Atom H1 is not in the residue template for MET #1 in chain ad  
Atom H1 is not in the residue template for MET #1 in chain bd  
Atom C1 is not in the residue template for GPC #101 in chain bd  
Atom H1 is not in the residue template for MET #1 in chain ae  
Atom H1 is not in the residue template for MET #1 in chain be  
Atom C1 is not in the residue template for GPC #101 in chain be  
Atom H1 is not in the residue template for MET #1 in chain af  
Atom H1 is not in the residue template for MET #1 in chain bf  
Atom C1 is not in the residue template for GPC #101 in chain bf  
Atom H1 is not in the residue template for MET #1 in chain ag  
Atom H1 is not in the residue template for MET #1 in chain bg  
Atom C1 is not in the residue template for GPC #101 in chain bg  
Atom H1 is not in the residue template for MET #1 in chain ah  
Atom H1 is not in the residue template for MET #1 in chain bh  
Atom C1 is not in the residue template for GPC #101 in chain bh  
Atom H1 is not in the residue template for MET #1 in chain ai  
Atom H1 is not in the residue template for MET #1 in chain bi  
Atom H1 is not in the residue template for MET #1 in chain aj  
Atom C1 is not in the residue template for GPC #101 in chain aj  
Atom H1 is not in the residue template for MET #1 in chain bj  
Atom C1 is not in the residue template for GPC #101 in chain bj  
Atom H1 is not in the residue template for MET #1 in chain ak  
Atom H1 is not in the residue template for MET #1 in chain bk  
Atom C1 is not in the residue template for GPC #101 in chain bk  
Atom H1 is not in the residue template for MET #1 in chain al  
Atom H1 is not in the residue template for MET #1 in chain bl  
Atom C1 is not in the residue template for GPC #101 in chain bl  
Atom H1 is not in the residue template for MET #1 in chain am  
Atom H1 is not in the residue template for MET #1 in chain bm  
Atom H1 is not in the residue template for MET #1 in chain an  
Atom C1 is not in the residue template for GPC #101 in chain an  
Atom H1 is not in the residue template for MET #1 in chain bn  
Atom C1 is not in the residue template for GPC #101 in chain bn  
Atom H1 is not in the residue template for MET #1 in chain ao  
Atom H1 is not in the residue template for MET #1 in chain bo  
Atom C1 is not in the residue template for GPC #101 in chain bo  
Atom H1 is not in the residue template for MET #1 in chain ap  
Atom H1 is not in the residue template for MET #1 in chain bp  
Atom C1 is not in the residue template for GPC #101 in chain bp  
Atom H1 is not in the residue template for ALA #1 in chain L  
Atom C1 is not in the residue template for GP1 #701 in chain M  
Atom H1 is not in the residue template for SER #1 in chain H2  
Atom H1 is not in the residue template for MET #1 in chain H1  
Atom CH1 is not in the residue template for TRP #47 in chain H1  
Atom H1 is not in the residue template for MET #3 in chain AA  
Atom H1 is not in the residue template for MET #1 in chain BA  
Atom C1 is not in the residue template for GPC #101 in chain BA  
Atom H1 is not in the residue template for MET #3 in chain AW  
Atom H1 is not in the residue template for MET #1 in chain BW  
Atom C1 is not in the residue template for GPC #101 in chain BW  
Atom H1 is not in the residue template for MET #3 in chain AX  
Atom H1 is not in the residue template for MET #1 in chain BX  
Atom C1 is not in the residue template for GPC #101 in chain BX  
Atom H1 is not in the residue template for MET #3 in chain AV  
Atom C1 is not in the residue template for GPC #101 in chain AV  
Atom H1 is not in the residue template for MET #1 in chain BV  
Atom H1 is not in the residue template for MET #3 in chain AU  
Atom H1 is not in the residue template for MET #1 in chain BU  
Atom C1 is not in the residue template for GPC #101 in chain BU  
Atom H1 is not in the residue template for MET #3 in chain AB  
Atom H1 is not in the residue template for MET #1 in chain BB  
Atom C1 is not in the residue template for GPC #101 in chain BB  
Atom H1 is not in the residue template for MET #3 in chain AC  
Atom H1 is not in the residue template for MET #1 in chain BC  
Atom C1 is not in the residue template for GPC #101 in chain BC  
Atom H1 is not in the residue template for MET #3 in chain AD  
Atom H1 is not in the residue template for MET #1 in chain BD  
Atom C1 is not in the residue template for GPC #101 in chain BD  
Atom H1 is not in the residue template for MET #3 in chain AE  
Atom H1 is not in the residue template for MET #1 in chain BE  
Atom C1 is not in the residue template for GPC #101 in chain BE  
Atom H1 is not in the residue template for MET #3 in chain BF  
Atom H1 is not in the residue template for MET #1 in chain AF  
Atom C1 is not in the residue template for GPC #101 in chain AF  
Atom H1 is not in the residue template for MET #3 in chain BG  
Atom H1 is not in the residue template for MET #1 in chain AG  
Atom C1 is not in the residue template for GPC #101 in chain AG  
Atom H1 is not in the residue template for MET #3 in chain AH  
Atom H1 is not in the residue template for MET #1 in chain BH  
Atom C1 is not in the residue template for GPC #101 in chain BH  
Atom H1 is not in the residue template for MET #3 in chain AI  
Atom H1 is not in the residue template for MET #1 in chain BI  
Atom C1 is not in the residue template for GPC #101 in chain BI  
Atom H1 is not in the residue template for MET #3 in chain AJ  
Atom H1 is not in the residue template for MET #1 in chain BJ  
Atom C1 is not in the residue template for GPC #101 in chain BJ  
Atom H1 is not in the residue template for MET #3 in chain AK  
Atom H1 is not in the residue template for MET #1 in chain BK  
Atom C1 is not in the residue template for GPC #101 in chain BK  
Atom H1 is not in the residue template for MET #3 in chain AL  
Atom H1 is not in the residue template for MET #1 in chain BL  
Atom C1 is not in the residue template for GPC #101 in chain BL  
Atom H1 is not in the residue template for MET #3 in chain AM  
Atom H1 is not in the residue template for MET #1 in chain BM  
Atom C1 is not in the residue template for GPC #101 in chain BM  
Atom H1 is not in the residue template for MET #3 in chain AN  
Atom H1 is not in the residue template for MET #1 in chain BN  
Atom C1 is not in the residue template for GPC #101 in chain BN  
Atom H1 is not in the residue template for MET #3 in chain AO  
Atom H1 is not in the residue template for MET #1 in chain BO  
Atom C1 is not in the residue template for GPC #101 in chain BO  
Atom H1 is not in the residue template for MET #3 in chain AP  
Atom H1 is not in the residue template for MET #1 in chain BP  
Atom C1 is not in the residue template for GPC #101 in chain BP  
Atom H1 is not in the residue template for MET #3 in chain AQ  
Atom H1 is not in the residue template for MET #1 in chain BQ  
Atom C1 is not in the residue template for GPC #101 in chain BQ  
Atom H1 is not in the residue template for MET #3 in chain AR  
Atom H1 is not in the residue template for MET #1 in chain BR  
Atom C1 is not in the residue template for GPC #101 in chain BR  
Atom H1 is not in the residue template for MET #3 in chain AS  
Atom H1 is not in the residue template for MET #1 in chain BS  
Atom C1 is not in the residue template for GPC #101 in chain BS  
Atom H1 is not in the residue template for MET #3 in chain AT  
Atom H1 is not in the residue template for MET #1 in chain BT  
Atom C1 is not in the residue template for GPC #101 in chain BT  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 90425  
Skipping chem_comp category: Missing column 'type' near line 90949  
Skipping chem_comp category: Missing column 'type' near line 91841  
Skipping chem_comp category: Missing column 'type' near line 91868  
Skipping chem_comp category: Missing column 'type' near line 92039  
  
Chain information for gprc-dlh1-car.cif #3  
---  
Chain | Description  
AA AB AC AD AE AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX BF BG | No
description available  
AF AG BA BB BC BD BE BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX ba bb
bc bd be bf bg bh bi bj bk bl bm bn bo bp | No description available  
C | No description available  
H1 | No description available  
H2 | No description available  
L | No description available  
M | No description available  
aa | No description available  
ab ac ad ae af ag ah ai aj ak al am an ao ap | No description available  
  

> select #3

89248 atoms, 90850 bonds, 354 pseudobonds, 3 models selected  

> style sel stick

Changed 89248 atom styles  

> select clear

> color #3 green

> hide H

> hide #!3 models

> show #!3 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show H&~HC

> select clear

> show #!2 models

> hide #!2 models

> isolde stepto

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

> isolde stepto

> isolde stepto

> isolde stepto

> usage isolde step

isolde stepto [residue] [viewDistance a number] [interpolateFrames
interpolateFrames] [polymericOnly true or false]  
— Step the view forward or backward through the chain, or jump to a specific
residue  
residue: a residues specifier or a text string  
interpolateFrames: an integer ≥ 1  

> isolde stepto interpolateFrames 0

Invalid "interpolateFrames" argument: Must be greater than 1or equal to  




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         10G         41G        352M         10G         51G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia

Change History (6)

comment:1 by Tom Goddard, 5 years ago

Component:	Unassigned → Command Line
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Garbled PostiveIntArg error message

comment:2 by Greg Couch, 5 years ago

So there are a couple of things in the log that need addressing.

(1) the incorrect error message -- the subject of this ticket, will fix that, and
(2) the incorrect Clipper session support -- do you want/have a ticket for that? Or should I send you email directly? The API is poorly documented.

-- Greg

comment:3 by Greg Couch, 5 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed the error message.

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

I raised the session save error as a separate ticket, and Tom filled me 
in. I'd been misunderstanding what the "version" key should refer to - 
at the time I wrote Clipper/ISOLDE's save/restore methods, every example 
bundle I looked at used CORE_STATE_VERSION, so I assumed (a bit 
stupidly, now I really think about it) that it was a reference to the 
version of the ChimeraX core save/restore code... anyway, will add 
version specifiers to Clipper and ISOLDE and adjust the code 
accordingly.

On 2020-05-22 21:40, ChimeraX wrote:

comment:5 by Greg Couch, 5 years ago

Yes, until it was recently fixed, many places in the code were incorrectly using the CORE_STATE_VERSION. There's also the issue of how it's related to the minimum and maximum session numbers in the bundle_info.xml file. In a session file, the bundles needed, along with their maximum session version number, are in a manifest at the beginning of the session. That maximum session version number should increase every time you change a data structure in a take_snapshot() incompatibly. That way, ChimeraX's with older versions of the bundle, will note that it needs to be updated before the session can be restored. Looking back, the maximum version number should be the sum of all of the version numbers in used in the various take_snapshots inside the bundle. But as long as it increases every time a change is made, you're golden.

in reply to: 6 ; follow-up: 6 comment:6 by Tristan Croll, 5 years ago

Thanks - that all makes sense.

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