Opened 5 years ago

Closed 5 years ago

#3246 closed defect (duplicate)

Write mmCIF: citation is None

Reported by: sitins07@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-05-07)
Description
Error during mmCIF file save. 

Log:
UCSF ChimeraX version: 1.0rc202005070439 (2020-05-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open X:/Work/Projects/48S/ChimeraX/closed/40S/40S-full.cif

Chain information for 40S-full.cif #1  
---  
Chain | Description  
SA | 40S ribosomal protein SA  
SB | 40S ribosomal protein S3a  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4, X isoform  
SF | 40S ribosomal protein S5  
SG | 40S ribosomal protein S6  
SH | 40S ribosomal protein S7  
SI | 40S ribosomal protein S8  
SJ | 40S ribosomal protein S9  
SK | 40S ribosomal protein S10  
SL | 40S ribosomal protein S11  
SM | 40S ribosomal protein S12  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16  
SR | 40S ribosomal protein S17  
SS | 40S ribosomal protein S18  
ST | 40S ribosomal protein S19  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21  
SW | 40S ribosomal protein S15a  
SX | 40S ribosomal protein S23  
SY | 40S ribosomal protein S24  
SZ | 40S ribosomal protein S25  
Sa | 40S ribosomal protein S26  
Sb | 40S ribosomal protein S27  
Sc | 40S ribosomal protein S28  
Sd | 40S ribosomal protein S29  
Se | 40S ribosomal protein S30  
  

> ui mousemode right select

Drag select of 36212 atoms, 12 pseudobonds  

> hide sel atoms

> show sel atoms

> style sel stick

Changed 36212 atom styles  

> select clear

> close #1

> open 6ek0

6ek0 title:  
High-resolution cryo-EM structure of the human 80S ribosome [more info...]  
  
Chain information for 6ek0 #1  
---  
Chain | Description  
L5 | 28S ribosomal RNA  
L7 | 5S ribosomal RNA  
L8 | 5.8S ribosomal RNA  
LA | 60S ribosomal protein L8  
LB | 60S ribosomal protein L3  
LC | 60S ribosomal protein L4  
LD | 60S ribosomal protein L5  
LE | 60S ribosomal protein L6  
LF | 60S ribosomal protein L7  
LG | 60S ribosomal protein L7a  
LH | 60S ribosomal protein L9  
LI | 60S ribosomal protein L10-like  
LJ | 60S ribosomal protein L11  
LL | 60S ribosomal protein L13  
LM | 60S ribosomal protein L14  
LN | 60S ribosomal protein L15  
LO | 60S ribosomal protein L13a  
LP | 60S ribosomal protein L17  
LQ | 60S ribosomal protein L18  
LR | 60S ribosomal protein L19  
LS | 60S ribosomal protein L18a  
LT | 60S ribosomal protein L21  
LU | 60S ribosomal protein L22  
LV | 60S ribosomal protein L23  
LW | 60S ribosomal protein L24  
LX | 60S ribosomal protein L23a  
LY | 60S ribosomal protein L26  
LZ | 60S ribosomal protein L27  
La | 60S ribosomal protein L27a  
Lb | 60S ribosomal protein L29  
Lc | 60S ribosomal protein L30  
Ld | 60S ribosomal protein L31  
Le | 60S ribosomal protein L32  
Lf | 60S ribosomal protein L35a  
Lg | 60S ribosomal protein L34  
Lh | 60S ribosomal protein L35  
Li | 60S ribosomal protein L36  
Lj | 60S ribosomal protein L37  
Lk | 60S ribosomal protein L38  
Ll | 60S ribosomal protein L39  
Lm | Ubiquitin-60S ribosomal protein L40  
Ln | 60S ribosomal protein L41  
Lo | 60S ribosomal protein L36a  
Lp | 60S ribosomal protein L37a  
Lr | 60S ribosomal protein L28  
Lz | 60S ribosomal protein L10a  
S2 | 18S ribosomal RNA  
S6 | Human initiator Met-tRNA-i  
SA | 40S ribosomal protein SA  
SB | 40S ribosomal protein S3a  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4, X isoform  
SF | 40S ribosomal protein S5  
SG | 40S ribosomal protein S6  
SH | 40S ribosomal protein S7  
SI | 40S ribosomal protein S8  
SJ | 40S ribosomal protein S9  
SK | 40S ribosomal protein S10  
SL | 40S ribosomal protein S11  
SM | 40S ribosomal protein S12  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16  
SR | 40S ribosomal protein S17  
SS | 40S ribosomal protein S18  
ST | 40S ribosomal protein S19  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21  
SW | 40S ribosomal protein S15a  
SX | 40S ribosomal protein S23  
SY | 40S ribosomal protein S24  
SZ | 40S ribosomal protein S25  
Sa | 40S ribosomal protein S26  
Sb | 40S ribosomal protein S27  
Sc | 40S ribosomal protein S28  
Sd | 40S ribosomal protein S29  
Se | 40S ribosomal protein S30  
Sf | Ubiquitin-40S ribosomal protein S27a  
Sg | Receptor of activated protein C kinase 1  
  
Non-standard residues in 6ek0 #1  
---  
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid  
HMT —
(3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine
(Homoharringtonine, Cephalotaxine, [3(R)]-4-methyl
2-hydroxy-2-(4-hydroxy-4-methylpentyl)butanedioate)  
HYG — hygromycin B (hygromix, antihelmycin, hydromycin B, destomysin,
antibiotic A-396-II)  
MG — magnesium ion  
ZN — zinc ion  
  

> select #1/SA-Se S2

Expected a keyword  

> select #1/SA-Se,S2

73334 atoms, 78115 bonds, 1619 pseudobonds, 4 models selected  

> cd X:/Work/Projects/48S/ChimeraX/closed/40S

Current working directory is: X:\Work\Projects\48S\ChimeraX\closed\40S  

> save 40S.cif models #1 slectedOnly 1

Expected a keyword  

> save 40S.cif models #1 selectedOnly true

> style sel stick

Changed 73334 atom styles  

> close #1

> open X:/Work/Projects/48S/ChimeraX/closed/40S/40S.cif

Chain information for 40S.cif #1  
---  
Chain | Description  
S2 | 18S ribosomal RNA  
SA | 40S ribosomal protein SA  
SB | 40S ribosomal protein S3a  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4, X isoform  
SF | 40S ribosomal protein S5  
SG | 40S ribosomal protein S6  
SH | 40S ribosomal protein S7  
SI | 40S ribosomal protein S8  
SJ | 40S ribosomal protein S9  
SK | 40S ribosomal protein S10  
SL | 40S ribosomal protein S11  
SM | 40S ribosomal protein S12  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16  
SR | 40S ribosomal protein S17  
SS | 40S ribosomal protein S18  
ST | 40S ribosomal protein S19  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21  
SW | 40S ribosomal protein S15a  
SX | 40S ribosomal protein S23  
SY | 40S ribosomal protein S24  
SZ | 40S ribosomal protein S25  
Sa | 40S ribosomal protein S26  
Sb | 40S ribosomal protein S27  
Sc | 40S ribosomal protein S28  
Sd | 40S ribosomal protein S29  
Se | 40S ribosomal protein S30  
  

> select /S2:1-1869

36938 atoms, 41283 bonds, 1458 pseudobonds, 3 models selected  

> show sel cartoons

> style sel stick

Changed 36938 atom styles  

> select clear

> select /SA:3-223

1741 atoms, 1778 bonds, 1 model selected  

> style sel stick

Changed 1741 atom styles  

> open X:/Work/Projects/48S/ChimeraX/closed/3d360_closedagain_c3_ctf_37A.ccp4

Opened 3d360_closedagain_c3_ctf_37A.ccp4, grid size 360,360,360, pixel 1.16,
shown at level 4.12, step 2, values float32  

> select #2

2 models selected  

> select #1

73334 atoms, 78115 bonds, 1619 pseudobonds, 4 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> fitmap sel inMap #2

Fit molecule 40S.cif (#1) to map 3d360_closedagain_c3_ctf_37A.ccp4 (#2) using
73334 atoms  
average map value = 6.704, steps = 100  
shifted from previous position = 6.34  
rotated from previous position = 5.89 degrees  
atoms outside contour = 21870, contour level = 4.1156  
  
Position of 40S.cif (#1) relative to 3d360_closedagain_c3_ctf_37A.ccp4 (#2)
coordinates:  
Matrix rotation and translation  
-0.18877163 0.02995264 0.98156411 -72.10489248  
0.57548814 0.81329067 0.08585851 -206.59569509  
-0.79572525 0.58108615 -0.17076359 377.10345921  
Axis 0.25740036 0.92376692 0.28354845  
Axis point 158.84293757 0.00000000 238.96018336  
Rotation angle (degrees) 105.85014507  
Shift along axis -102.47899209  
  

> ui mousemode right select

> select clear

> save 40S.cif models #1

Traceback (most recent call last):  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 124, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 139, in write_mmcif  
save_structure(session, f, [m], [xforms[m]], used_data_names, selected_only,
displayed_only)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 303, in save_structure  
citation.print(file, fixed_width=True)  
AttributeError: 'NoneType' object has no attribute 'print'  
  
AttributeError: 'NoneType' object has no attribute 'print'  
  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 303, in save_structure  
citation.print(file, fixed_width=True)  
  
See log for complete Python traceback.  
  

> save 40S-1.cif models #1

Traceback (most recent call last):  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 124, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 139, in write_mmcif  
save_structure(session, f, [m], [xforms[m]], used_data_names, selected_only,
displayed_only)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 303, in save_structure  
citation.print(file, fixed_width=True)  
AttributeError: 'NoneType' object has no attribute 'print'  
  
AttributeError: 'NoneType' object has no attribute 'print'  
  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 303, in save_structure  
citation.print(file, fixed_width=True)  
  
See log for complete Python traceback.  
  

> save 40S-1.cif models #1

Traceback (most recent call last):  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 124, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 139, in write_mmcif  
save_structure(session, f, [m], [xforms[m]], used_data_names, selected_only,
displayed_only)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 303, in save_structure  
citation.print(file, fixed_width=True)  
AttributeError: 'NoneType' object has no attribute 'print'  
  
AttributeError: 'NoneType' object has no attribute 'print'  
  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 303, in save_structure  
citation.print(file, fixed_width=True)  
  
See log for complete Python traceback.  
  

> select #1

73334 atoms, 78115 bonds, 1619 pseudobonds, 4 models selected  

> save X:/Work/Projects/48S/ChimeraX/closed/40S/40S-1.cif

Traceback (most recent call last):  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 162, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 453, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1660, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 38, in run_provider  
providers.run_provider(session, name)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider  
what(session)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 122, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 49, in display  
run(session, cmd)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 124, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 139, in write_mmcif  
save_structure(session, f, [m], [xforms[m]], used_data_names, selected_only,
displayed_only)  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 303, in save_structure  
citation.print(file, fixed_width=True)  
AttributeError: 'NoneType' object has no attribute 'print'  
  
AttributeError: 'NoneType' object has no attribute 'print'  
  
File "X:\Soft\ChimeraX\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 303, in save_structure  
citation.print(file, fixed_width=True)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 445.87
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GE73VR 7RF
OS: Майкрософт Windows 10 Pro (Build 18363)
Memory: 17,059,950,592
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Write mmCIF: citation is None

comment:2 by Greg Couch, 5 years ago

Resolution: → duplicate
Status: assigned → closed

Duplicate of #3204 that was fixed on May 13th. Please download a newer release candidate.

Note: See TracTickets for help on using tickets.