Opened 6 years ago

Closed 5 years ago

Last modified 5 years ago

#3047 closed defect (fixed)

Problem writing 'software' info to mmCIF

Reported by: philipp.milkereit@… Owned by: Greg Couch
Priority: normal Milestone: 1.0
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: 0.94 (2020-04-14)
Description
The save2 and save commands using the mmcif format option  caused problems with a specific mmcif model fetched from the RCSB database (3jct). The same procedure worked fine with other mmcif files.


Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.94.dev202004140658 (2020-04-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open E:\Chimera_Nog1\Nog1_Wt\Nog1_C_job127_Nog2Like\3jct.cif

3jct.cif title:  
Cryo-em structure of eukaryotic pre-60S ribosomal subunits [more info...]  
  
Chain information for 3jct.cif #1  
---  
Chain | Description  
1 | RDN25-1 rRNA  
2 | RDN58-1 rRNA  
3 | RDN5-2 rRNA  
4 | Probable metalloprotease ARX1  
5 | rRNA-processing protein CGR1  
6 | ITS2-1 miscRNA  
A | 60S ribosomal protein L2-A  
B | 60S ribosomal protein L3  
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 | Bud site selection protein 20  
J | 60S ribosomal protein L11-A  
K | Proteasome-interacting protein CIC1  
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  
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 | Ribosome assembly factor MRT4  
X | 60S ribosomal protein L25  
Y | 60S ribosomal protein L26-A  
Z | 60S ribosomal protein L27-A  
a | 60S ribosomal protein L28  
b | Nucleolar GTP-binding protein 1  
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 | Nucleolar GTP-binding protein 2  
n | Pescadillo homolog  
o | Ribosome biogenesis protein 15  
p | 60S ribosomal protein L43-A  
q | Ribosome biogenesis protein NOP53  
r | Ribosome biogenesis protein NSA2  
s | Nuclear GTP-binding protein NUG1  
t | Ribosome biogenesis protein RLP7  
u | Ribosome biogenesis protein RLP24  
v | Ribosome biogenesis protein RPF2  
w | Regulator of ribosome biosynthesis  
x | Ribosome assembly protein 4  
y | Eukaryotic translation initiation factor 6  
z | UPF0642 protein YBL028C  
  
Non-standard residues in 3jct.cif #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> toolshed show "Build Structure"

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

> style ball

Changed 156562 atom styles  

> lighting simple

> toolshed show Shell

> select clear

> select up

2 atoms, 1 bond, 1 model selected  

> select up

8 atoms, 7 bonds, 1 model selected  

> select up

14 atoms, 13 bonds, 1 model selected  

> select up

743 atoms, 751 bonds, 1 model selected  

> open E:\Chimera_Nog1\Nog1_Wt\Nog1_C_job127_Nog2Like\map\Job127_class001.mrc

Opened Job127_class001.mrc, grid size 400,400,400, pixel 1.06, shown at level
0.0373, step 2, values float32  

> open2
> E:/Chimera_Nog1/Nog1_Wt/Nog1_C_job127_Nog2Like/3jct_Nog2_FitToJob127.pdb

Ignored bad PDB record found on line 157395  
END  
  

Chain information for 3jct_Nog2_FitToJob127.pdb #3  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | 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  
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  
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  
  

> mmaker #1 #3

Missing required "to" argument  

> mmaker #1 to #3

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 3jct_Nog2_FitToJob127.pdb, chain b (#3) with 3jct.cif, chain b
(#1), sequence alignment score = 3276.4  
RMSD between 642 pruned atom pairs is 0.001 angstroms; (across all 642 pairs:
0.001)  
  

> hide #!3 models

> volume #2 step 1

> volume #2 level 0.02605

> lighting simple

> toolshed show "Fit in Map"

Fit molecule 3jct.cif (#1) to map Job127_class001.mrc (#2) using 156562 atoms  
average map value = 0.04212, steps = 40  
shifted from previous position = 0.015  
rotated from previous position = 0.00269 degrees  
atoms outside contour = 44181, contour level = 0.026052  
  
Position of 3jct.cif (#1) relative to Job127_class001.mrc (#2) coordinates:  
Matrix rotation and translation  
0.04043773 0.92217240 0.38465940 -77.58804920  
-0.84270868 0.23831880 -0.48274863 434.75063513  
-0.53684902 -0.30463455 0.78675976 222.64199088  
Axis 0.08910486 0.46100163 -0.88291439  
Axis point 227.67156759 320.74246872 0.00000000  
Rotation angle (degrees) 88.12276108  
Shift along axis -3.06654050  
  
Fit molecule 3jct.cif (#1) to map Job127_class001.mrc (#2) using 156562 atoms  
average map value = 0.04212, steps = 40  
shifted from previous position = 0.0118  
rotated from previous position = 0.0014 degrees  
atoms outside contour = 44199, contour level = 0.026052  
  
Position of 3jct.cif (#1) relative to Job127_class001.mrc (#2) coordinates:  
Matrix rotation and translation  
0.04041535 0.92217631 0.38465237 -77.59022906  
-0.84271277 0.23829563 -0.48275292 434.76137560  
-0.53684428 -0.30464083 0.78676056 222.65042289  
Axis 0.08910380 0.46099540 -0.88291775  
Axis point 227.67194851 320.74881056 0.00000000  
Rotation angle (degrees) 88.12404357  
Shift along axis -3.07259997  
  

> save 3jct_Nog2_FitToJob127_cif format mmcif models #1 relModel #2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 229, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 63, in save_file  
return mmcif_write.write_mmcif(session, path, models=models,
rel_model=rel_model, selected_only=selected_only,
displayed_only=displayed_only)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
  
See log for complete Python traceback.  
  

> save 3jct_Nog2_FitToJob127_cif.cif format mmcif models #1 relModel #2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 229, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 63, in save_file  
return mmcif_write.write_mmcif(session, path, models=models,
rel_model=rel_model, selected_only=selected_only,
displayed_only=displayed_only)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
  
See log for complete Python traceback.  
  

> save 3jct_Nog2_FitToJob127_cif format pdb models #1 relModel #2

Invalid "format" argument: Should be one of 'aln', 'bmp', 'brix', 'cmap',
'dcd', 'fasta', 'gif', 'gltf', 'imagic', 'jpeg', 'markers', 'mmcif', 'mol2',
'mrc', 'obj', 'pdb', 'pir', 'png', 'ppm', 'pseudobonds', 'segger', 'session',
'stl', 'tiff', 'vtk', or 'x3d'  

> save 3jct_Nog2_FitToJob127_cif format mmcif models #1 relModel #2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 229, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 63, in save_file  
return mmcif_write.write_mmcif(session, path, models=models,
rel_model=rel_model, selected_only=selected_only,
displayed_only=displayed_only)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
  
See log for complete Python traceback.  
  

> save 3jct_Nog2_FitToJob127_cif format mmcif models #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 229, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 63, in save_file  
return mmcif_write.write_mmcif(session, path, models=models,
rel_model=rel_model, selected_only=selected_only,
displayed_only=displayed_only)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
  
See log for complete Python traceback.  
  

> save 3jct_Nog2_FitToJob127_cif format mmcif

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 229, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 63, in save_file  
return mmcif_write.write_mmcif(session, path, models=models,
rel_model=rel_model, selected_only=selected_only,
displayed_only=displayed_only)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
  
See log for complete Python traceback.  
  

Missing "format" keyword's argument  

> save 3jct_Nog2_FitToJob127_cif format mmcif

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 229, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 63, in save_file  
return mmcif_write.write_mmcif(session, path, models=models,
rel_model=rel_model, selected_only=selected_only,
displayed_only=displayed_only)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
  
See log for complete Python traceback.  
  

> save 3jct_Nog2_FitToJob127_cif.cif models #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 229, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 63, in save_file  
return mmcif_write.write_mmcif(session, path, models=models,
rel_model=rel_model, selected_only=selected_only,
displayed_only=displayed_only)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
  
See log for complete Python traceback.  
  

> save 3jct_Nog2_FitToJob127_cif.mmcif models #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 229, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 63, in save_file  
return mmcif_write.write_mmcif(session, path, models=models,
rel_model=rel_model, selected_only=selected_only,
displayed_only=displayed_only)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\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 3jct_Nog2_FitToJob127_cif.mmcif models #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 115, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\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 3jct_Nog2_FitToJob127_cif.cif models #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 115, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\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 3jct_Nog2_FitToJob127_cif.cif format mmcif models #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 115, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
  
See log for complete Python traceback.  
  

> close #3

> close #2

> close #1

> open2 E:/Chimera_Nog1/Nog1_Wt/Nog1_C_job127_Nog2Like/3jct.cif

3jct.cif title:  
Cryo-em structure of eukaryotic pre-60S ribosomal subunits [more info...]  
  
Chain information for 3jct.cif #1  
---  
Chain | Description  
1 | RDN25-1 rRNA  
2 | RDN58-1 rRNA  
3 | RDN5-2 rRNA  
4 | Probable metalloprotease ARX1  
5 | rRNA-processing protein CGR1  
6 | ITS2-1 miscRNA  
A | 60S ribosomal protein L2-A  
B | 60S ribosomal protein L3  
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 | Bud site selection protein 20  
J | 60S ribosomal protein L11-A  
K | Proteasome-interacting protein CIC1  
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  
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 | Ribosome assembly factor MRT4  
X | 60S ribosomal protein L25  
Y | 60S ribosomal protein L26-A  
Z | 60S ribosomal protein L27-A  
a | 60S ribosomal protein L28  
b | Nucleolar GTP-binding protein 1  
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 | Nucleolar GTP-binding protein 2  
n | Pescadillo homolog  
o | Ribosome biogenesis protein 15  
p | 60S ribosomal protein L43-A  
q | Ribosome biogenesis protein NOP53  
r | Ribosome biogenesis protein NSA2  
s | Nuclear GTP-binding protein NUG1  
t | Ribosome biogenesis protein RLP7  
u | Ribosome biogenesis protein RLP24  
v | Ribosome biogenesis protein RPF2  
w | Regulator of ribosome biosynthesis  
x | Ribosome assembly protein 4  
y | Eukaryotic translation initiation factor 6  
z | UPF0642 protein YBL028C  
  
Non-standard residues in 3jct.cif #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> save2 3jct_Nog2_FitToJob127_cif.cif format mmcif models #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 115, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif.py", line 660, in _add_software  
if software.field_has('name', name):  
  
See log for complete Python traceback.  
  

Invalid "fromDatabase" argument: Should be one of 'cellpack', 'eds',
'edsdiff', 'emdb', 'ftp', 'http', 'https', 'pdb', 'pdbdev', 'pdbe',
'pdbe_updated', 'pdbj', 'pubchem', 'smiles', or 'uniprot'  

> open 6G5I fromDatabase pdb

Summary of feedback from opening 6G5I fetched from pdb  
---  
note | Fetching compressed mmCIF 6g5i from
http://files.rcsb.org/download/6g5i.cif  
  
6g5i title:  
Cryo-EM structure of a late human pre-40S ribosomal subunit - State R [more
info...]  
  
Chain information for 6g5i #2  
---  
Chain | Description  
2 | 18S ribosomal RNA  
A | 40S ribosomal protein SA  
B | 40S ribosomal protein S3a  
C | 40S ribosomal protein S2  
D | 40S ribosomal protein S3  
E | 40S ribosomal protein S4, X isoform  
F | 40S ribosomal protein S5  
G | 40S ribosomal protein S6  
H | 40S ribosomal protein S7  
I | 40S ribosomal protein S8  
J | 40S ribosomal protein S9  
K | 40S ribosomal protein S10  
L | 40S ribosomal protein S11  
M | 40S ribosomal protein S12  
N | 40S ribosomal protein S13  
O | 40S ribosomal protein S14  
P | 40S ribosomal protein S15  
Q | 40S ribosomal protein S16  
R | 40S ribosomal protein S17  
S | 40S ribosomal protein S18  
T | 40S ribosomal protein S19  
U | 40S ribosomal protein S20  
V | 40S ribosomal protein S21  
W | 40S ribosomal protein S15a  
X | 40S ribosomal protein S23  
Y | 40S ribosomal protein S24  
Z | 40S ribosomal protein S25  
b | 40S ribosomal protein S27  
c | 40S ribosomal protein S28  
d | 40S ribosomal protein S29  
e | 40S ribosomal protein S30  
f | Ribosomal protein S27a  
g | Receptor of activated protein C kinase 1  
x | RNA-binding protein PNO1  
y | RNA-binding protein NOB1  
z | Serine/threonine-protein kinase RIO1  
  
Non-standard residues in 6g5i #2  
---  
ZN — zinc ion  
  
  

> hide #!1 models

> select #2/2:1719@O2'

1 atom, 1 model selected  

> select up

22 atoms, 24 bonds, 1 model selected  

> select up

35380 atoms, 39560 bonds, 1 model selected  

> select clear

> save2 6g5i_cif.cif format mmcif models #2

> select up

Nothing selected  

> select up

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> open 3jct fromDatabase pdb

Summary of feedback from opening 3jct fetched from pdb  
---  
note | Fetching compressed mmCIF 3jct from
http://files.rcsb.org/download/3jct.cif  
  
3jct title:  
Cryo-em structure of eukaryotic pre-60S ribosomal subunits [more info...]  
  
Chain information for 3jct #3  
---  
Chain | Description  
1 | RDN25-1 rRNA  
2 | RDN58-1 rRNA  
3 | RDN5-2 rRNA  
4 | Probable metalloprotease ARX1  
5 | rRNA-processing protein CGR1  
6 | ITS2-1 miscRNA  
A | 60S ribosomal protein L2-A  
B | 60S ribosomal protein L3  
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 | Bud site selection protein 20  
J | 60S ribosomal protein L11-A  
K | Proteasome-interacting protein CIC1  
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  
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 | Ribosome assembly factor MRT4  
X | 60S ribosomal protein L25  
Y | 60S ribosomal protein L26-A  
Z | 60S ribosomal protein L27-A  
a | 60S ribosomal protein L28  
b | Nucleolar GTP-binding protein 1  
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 | Nucleolar GTP-binding protein 2  
n | Pescadillo homolog  
o | Ribosome biogenesis protein 15  
p | 60S ribosomal protein L43-A  
q | Ribosome biogenesis protein NOP53  
r | Ribosome biogenesis protein NSA2  
s | Nuclear GTP-binding protein NUG1  
t | Ribosome biogenesis protein RLP7  
u | Ribosome biogenesis protein RLP24  
v | Ribosome biogenesis protein RPF2  
w | Regulator of ribosome biosynthesis  
x | Ribosome assembly protein 4  
y | Eukaryotic translation initiation factor 6  
z | UPF0642 protein YBL028C  
  
Non-standard residues in 3jct #3  
---  
MG — magnesium ion  
ZN — zinc ion  
  
  

> save2 3jct_cif.cif format mmcif models #3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 115, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 302, in save_structure  
metadata=best_metadata)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\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: 3.3.0 NVIDIA 388.13
OpenGL renderer: GeForce GTX 750 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z170X-UD3
OS: Microsoft Windows 10 Home (Build 18362)
Memory: 17,133,551,616
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6600 CPU @ 3.30GHz"

Change History (4)

comment:1 by pett, 6 years ago

Component: Unassigned → Input/Output
Milestone: → 1.0
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem writing 'software' info to mmCIF

comment:2 by Greg Couch, 5 years ago

Fixed. The problem was due the fact that 3jct didn't already have a software table.

comment:3 by Greg Couch, 5 years ago

Resolution: → fixed
Status: assigned → closed

in reply to:  4 ; comment:4 by philipp.milkereit@…, 5 years ago 

Dear Greg,

thanks for your effort! Chimerax is a fantastic software! 
Should I try to o fix the error in the 3jct file, or will chimerax be able to handle that kind of incomplete files in a future version?

Best Philipp

-----Ursprüngliche Nachricht-----
Von: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Gesendet: Donnerstag, 23. April 2020 20:13
An: undisclosed-recipients:
Cc: gregc@cgl.ucsf.edu; philipp.milkereit@vkl.uni-regensburg.de
Betreff: [EXT] Re: [ChimeraX] #3047: Problem writing 'software' info to mmCIF

#3047: Problem writing 'software' info to mmCIF
------------------------------------------+------------------------
          Reporter:  philipp.milkereit@…  |      Owner:  Greg Couch
              Type:  defect               |     Status:  assigned
          Priority:  normal               |  Milestone:  1.0
         Component:  Input/Output         |    Version:
        Resolution:                       |   Keywords:
        Blocked By:                       |   Blocking:
Notify when closed:                       |   Platform:  all
           Project:  ChimeraX             |
------------------------------------------+------------------------

Comment (by Greg Couch):

 Fixed.  The problem was due the fact that 3jct didn't already have a  software table.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3047#comment:2>
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