Opened 5 years ago

Closed 5 years ago

#3396 closed defect (duplicate)

Saving mmCIF: 'software' is None

Reported by: h.shrma@… 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:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-04-22)
Description
saving a mmcif file

Log:
UCSF ChimeraX version: 0.94.dev202004220145 (2020-04-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open2
> /Users/himanshu/Documents/Science/documentation/Presentations/MIMS_SCIEITIFIC_EXCHANGE/6gqv_80s_trnacomplex.cif

Summary of feedback from opening
/Users/himanshu/Documents/Science/documentation/Presentations/MIMS_SCIEITIFIC_EXCHANGE/6gqv_80s_trnacomplex.cif  
---  
notes | Fetching CCD GCP from http://ligand-
expo.rcsb.org/reports/G/GCP/GCP.cif  
Fetching CCD DDE from http://ligand-expo.rcsb.org/reports/D/DDE/DDE.cif  
  
6gqv_80s_trnacomplex.cif title:  
Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and
eEF2 (GMPPCP) [more info...]  
  
Chain information for 6gqv_80s_trnacomplex.cif #1  
---  
Chain | Description  
1 | 25S ribosomal RNA  
2 | 18S ribosomal RNA  
3 | 5S ribosomal RNA  
4 | 5.8S ribosomal RNA  
A | 60S ribosomal protein L2-A  
AA | 40S ribosomal protein S10-A  
AB | 40S ribosomal protein S11-A  
AC | 40S ribosomal protein S12  
AD | 40S ribosomal protein S13  
AE | 40S ribosomal protein S14-B  
AF | 40S ribosomal protein S15  
AG | 40S ribosomal protein S16-A  
AH | 40S ribosomal protein S17-B  
AI | 40S ribosomal protein S18-A  
AJ | 40S ribosomal protein S19-A  
AK | 40S ribosomal protein S20  
AL | 40S ribosomal protein S21-A  
AM | 40S ribosomal protein S22-A  
AN | 40S ribosomal protein S23-A  
AO | 40S ribosomal protein S24-A  
AP | 40S ribosomal protein S25-A  
AQ | 40S ribosomal protein S26-B  
AR | 40S ribosomal protein S27-A  
AS | 40S ribosomal protein S28-A  
AT | 40S ribosomal protein S29-A  
AU | 40S ribosomal protein S30-A  
AV | Guanine nucleotide-binding protein subunit beta-like protein  
AW | Ubiquitin-40S ribosomal protein S31  
AX | Elongation factor 2  
AY | Transfer RNA - Phe  
AZ | Messenger RNA  
B | 60S ribosomal protein L3  
BA | 60S ribosomal protein L1-A  
C | 60S ribosomal protein L4-A  
D | 60S ribosomal protein L5  
E | 60S ribosomal protein L6-A  
F | 60S ribosomal protein L7-A  
G | 60S ribosomal protein L8-A  
H | 60S ribosomal protein L9-A  
I | 60S ribosomal protein L10  
J | 60S ribosomal protein L11-B  
L | 60S ribosomal protein L13-A  
M | 60S ribosomal protein L14-A  
N | 60S ribosomal protein L15-A  
O | 60S ribosomal protein L16-A  
P | 60S ribosomal protein L17-A  
P0 | 60S acidic ribosomal protein P0  
P2 | 60S ribosomal protein L12-A  
Q | 60S ribosomal protein L18-A  
R | 60S ribosomal protein L19-A  
S | 60S ribosomal protein L20-A  
T | 60S ribosomal protein L21-A  
U | 60S ribosomal protein L22-A  
V | 60S ribosomal protein L23-A  
W | 60S ribosomal protein L24-A  
X | 60S ribosomal protein L25  
Y | 60S ribosomal protein L26-A  
Z | 60S ribosomal protein L27-A  
a | 60S ribosomal protein L28  
b | 60S ribosomal protein L29  
c | 60S ribosomal protein L30  
d | 60S ribosomal protein L31-A  
e | 60S ribosomal protein L32  
f | 60S ribosomal protein L33-A  
g | 60S ribosomal protein L34-A  
h | 60S ribosomal protein L35-A  
i | 60S ribosomal protein L36-A  
j | 60S ribosomal protein L37-A  
k | 60S ribosomal protein L38  
l | 60S ribosomal protein L39  
m | Ubiquitin-60S ribosomal protein L40  
n | 60S ribosomal protein L41-B  
o | 60S ribosomal protein L42-A  
p | 60S ribosomal protein L43-A  
q | 40S ribosomal protein S0-A  
r | 40S ribosomal protein S1-A  
s | 40S ribosomal protein S2  
t | 40S ribosomal protein S3  
u | 40S ribosomal protein S4-A  
v | 40S ribosomal protein S5  
w | 40S ribosomal protein S6-A  
x | 40S ribosomal protein S7-A  
y | 40S ribosomal protein S8-A  
z | 40S ribosomal protein S9-A  
  
Non-standard residues in 6gqv_80s_trnacomplex.cif #1  
---  
GCP — phosphomethylphosphonic acid guanylate ester  
ZN — zinc ion  
  

> hide atoms

> show cartoons

> select /AX:3-839

6523 atoms, 6648 bonds, 1 model selected  

> delete atoms sel

> delete bonds sel

> sequence chain #1/m

Alignment identifier is 1.m  

> select /m:77-128

417 atoms, 423 bonds, 1 model selected  

> select /AV:2-319

2437 atoms, 2490 bonds, 1 model selected  

> select /AV:2-319

2437 atoms, 2490 bonds, 1 model selected  

> select /AV:2-319

2437 atoms, 2490 bonds, 1 model selected  

> sequence chain #1/AV

Alignment identifier is 1.AV  

> delete atoms sel

> delete bonds sel

> select /AW:116-152

287 atoms, 292 bonds, 1 model selected  

> sequence chain #1/AW

Alignment identifier is 1.AW  

> bgcOLOR WHITE

Unknown command: bgcOLOR WHITE  

> bgcolor white

Unknown command: bgcolor white  

> backgroundcolor

Unknown command: backgroundcolor  

> bgcolor

Unknown command: bgcolor  
Drag select of 3 pseudobonds, 3673 residues  
Drag select of 3 pseudobonds, 6445 residues  

> select up

113541 atoms, 123323 bonds, 3 pseudobonds, 2 models selected  

> select up

119006 atoms, 128892 bonds, 3 pseudobonds, 2 models selected  

> select up

203098 atoms, 218225 bonds, 9 pseudobonds, 2 models selected  

> select down

119006 atoms, 128892 bonds, 3 pseudobonds, 2 models selected  

> select ~sel

84092 atoms, 89333 bonds, 1559 pseudobonds, 4 models selected  

> select ~sel

119006 atoms, 128892 bonds, 3254 pseudobonds, 4 models selected  

> current sel

Unknown command: current sel  

> cartoon hide (#!1 & sel)

Drag select of 335 residues  

> select up

4136 atoms, 4204 bonds, 1 model selected  

> select up

6903 atoms, 7024 bonds, 1 model selected  

> select up

203098 atoms, 218225 bonds, 1 model selected  

> select up

203098 atoms, 218225 bonds, 1 model selected  

> select up

203098 atoms, 218225 bonds, 1 model selected  

> select down

6903 atoms, 7024 bonds, 1 model selected  

> cartoon hide sel

Drag select of 94 residues  

> cartoon hide sel

> save2
> /Users/himanshu/Documents/Science/documentation/Presentations/MIMS_SCIEITIFIC_EXCHANGE/6gqv_40Sonly.cif

Traceback (most recent call last):  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1460, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 90, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 101, in show_save_file_dialog  
_dlg.display(session, session.ui.main_window)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 31, in display  
run(session, cmd)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 115, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
AttributeError: 'NoneType' object has no attribute 'field_has'  
  
AttributeError: 'NoneType' object has no attribute 'field_has'  
  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
  
See log for complete Python traceback.  
  

> open2
> /Users/himanshu/Documents/Science/documentation/Presentations/MIMS_SCIEITIFIC_EXCHANGE/6gqv_40Sonly.cif

Drag select of 4 pseudobonds, 6685 residues  

> save2
> /Users/himanshu/Documents/Science/documentation/Presentations/MIMS_SCIEITIFIC_EXCHANGE/6gqv_40Sonly.cif

Traceback (most recent call last):  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1460, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 90, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 101, in show_save_file_dialog  
_dlg.display(session, session.ui.main_window)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 31, in display  
run(session, cmd)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 115, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
AttributeError: 'NoneType' object has no attribute 'field_has'  
  
AttributeError: 'NoneType' object has no attribute 'field_has'  
  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
  
See log for complete Python traceback.  
  

> save2
> /Users/himanshu/Documents/Science/documentation/Presentations/MIMS_SCIEITIFIC_EXCHANGE/6gqv40Sonly.cif

Traceback (most recent call last):  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1460, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 90, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 101, in show_save_file_dialog  
_dlg.display(session, session.ui.main_window)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 31, in display  
run(session, cmd)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 115, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
AttributeError: 'NoneType' object has no attribute 'field_has'  
  
AttributeError: 'NoneType' object has no attribute 'field_has'  
  
File
"/Users/himanshu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.21
OpenGL renderer: AMD Radeon Pro 570 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (3)

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 → Saving mmCIF: 'software' is None

comment:2 by Greg Couch, 5 years ago

Status: assigned → accepted

comment:3 by Greg Couch, 5 years ago

Resolution: → duplicate
Status: accepted → closed

This is actually a duplicate of #3204 and has been fixed.

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