Opened 5 years ago

Closed 3 years ago

#3613 closed defect (fixed)

ISOLDE: cannot import name 'save' from 'chimerax.core.commands'

Reported by: christl.gaubitz@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Eric Pettersen
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 (2020-06-04 23:15:07 UTC)
Description
Isolde's Save current model as... gives following error message:
ImportError: cannot import name 'save' from 'chimerax.core.commands' (C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\commands\__init__.py)

File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-packages\chimerax\isolde\isolde.py", line 1177, in save_cif_file
from chimerax.core.commands import save

See log for complete Python traceback.


Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/Christl/Dropbox (UMass Medical School)/yRFC-
> building/denmod_map.ccp4" "C:/Users/Christl/Dropbox (UMass Medical
> School)/yRFC-building/DNA1_rigidbodyfitted-coot-1-loopFitted.pdb"

Chain information for DNA1_rigidbodyfitted-coot-1-loopFitted.pdb #2  
---  
Chain | Description  
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  
  
Opened denmod_map.ccp4, grid size 240,240,240, pixel 1.06, shown at level 1.2,
step 1, values float32  

> set bgColor white

> hide atoms

> show cartoons

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for DNA1_rigidbodyfitted-coot-1-loopFitted.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
2.2/C | No description available  
2.2/D | No description available  
2.2/E | No description available  
2.2/F | No description available  
2.2/G | No description available  
2.2/H | No description available  
2.2/I | No description available  
2.2/J | No description available  
  
Done loading forcefield  

> select #1/ A:412

Nothing selected  

> select #1/ A:410

Nothing selected  

> select #2/ A:412

9 atoms, 8 bonds, 1 model selected  

> view #2/ A:412

> addh

Summary of feedback from adding hydrogens to DNA1_rigidbodyfitted-
coot-1-loopFitted.pdb #2.2  
---  
notes | No usable SEQRES records for DNA1_rigidbodyfitted-
coot-1-loopFitted.pdb (#2.2) chain A; guessing termini instead  
No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted.pdb (#2.2)
chain B; guessing termini instead  
No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted.pdb (#2.2)
chain C; guessing termini instead  
No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted.pdb (#2.2)
chain D; guessing termini instead  
No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted.pdb (#2.2)
chain E; guessing termini instead  
5 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A VAL 291, /B THR 4, /C SER
9, /D SER 14, /E TRP 4, /F MET 1, /G MET 1, /H MET 1, /I DT 5, /J DA 3  
Chain-initial residues that are not actual N termini: /E HIS 133, /G GLU 189,
/H GLU 130  
Chain-final residues that are actual C termini: /I DT 28, /J DA 20  
Chain-final residues that are not actual C termini: /A MET 777, /B LYS 322, /C
THR 335, /D LEU 353, /E LEU 353, /E GLU 120, /F ASN 255, /G ASN 255, /G ASP
187, /H LYS 253, /H ASP 120  
2211 hydrogen bonds  
Adding 'H' to /E HIS 133  
Adding 'H' to /G GLU 189  
Adding 'H' to /H GLU 130  
/A MET 777 is not terminus, removing H atom from 'C'  
/B LYS 322 is not terminus, removing H atom from 'C'  
/C THR 335 is not terminus, removing H atom from 'C'  
/D LEU 353 is not terminus, removing H atom from 'C'  
/E LEU 353 is not terminus, removing H atom from 'C'  
5 messages similar to the above omitted  
21175 hydrogens added  
  
Loading residue template for ADP from internal database  
Loading residue template for AGS from internal database  

> hide HC

> close #2

Deleting atomic symmetry model...  

> open "C:/Users/Christl/Dropbox (UMass Medical School)/yRFC-
> building/DNA1_rigidbodyfitted-coot-1-loopFitted-NoATPDNA.pdb"

Chain information for DNA1_rigidbodyfitted-coot-1-loopFitted-NoATPDNA.pdb #1  
---  
Chain | Description  
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  
  
Chain information for DNA1_rigidbodyfitted-coot-1-loopFitted-NoATPDNA.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
  

> open "C:/Users/Christl/Dropbox (UMass Medical School)/yRFC-
> building/denmod_map.ccp4"

Opened denmod_map.ccp4, grid size 240,240,240, pixel 1.06, shown at level 1.2,
step 1, values float32  

> addh

Summary of feedback from adding hydrogens to DNA1_rigidbodyfitted-
coot-1-loopFitted-NoATPDNA.pdb #1.2  
---  
notes | No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted-
NoATPDNA.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted-
NoATPDNA.pdb (#1.2) chain B; guessing termini instead  
No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted-
NoATPDNA.pdb (#1.2) chain C; guessing termini instead  
No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted-
NoATPDNA.pdb (#1.2) chain D; guessing termini instead  
No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted-
NoATPDNA.pdb (#1.2) chain E; guessing termini instead  
3 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A VAL 291, /B THR 4, /C SER
9, /D SER 14, /E TRP 4, /F MET 1, /G MET 1, /H MET 1  
Chain-initial residues that are not actual N termini: /E HIS 133, /G GLU 189,
/H GLU 130  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A MET 777, /B LYS 322, /C
THR 335, /D LEU 353, /E LEU 353, /E GLU 120, /F ASN 255, /G ASN 255, /G ASP
187, /H LYS 253, /H ASP 120  
2102 hydrogen bonds  
Adding 'H' to /E HIS 133  
Adding 'H' to /G GLU 189  
Adding 'H' to /H GLU 130  
/A MET 777 is not terminus, removing H atom from 'C'  
/B LYS 322 is not terminus, removing H atom from 'C'  
/C THR 335 is not terminus, removing H atom from 'C'  
/D LEU 353 is not terminus, removing H atom from 'C'  
/E LEU 353 is not terminus, removing H atom from 'C'  
5 messages similar to the above omitted  
20633 hydrogens added  
  

> hide HC

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  

> select clear

Traceback (most recent call last):  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1165, in _save_cif_file  
self.save_cif_file(self._selected_model, filename)  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1177, in save_cif_file  
from chimerax.core.commands import save  
ImportError: cannot import name 'save' from 'chimerax.core.commands'
(C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\\__init__.py)  
  
ImportError: cannot import name 'save' from 'chimerax.core.commands'
(C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\\__init__.py)  
  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1177, in save_cif_file  
from chimerax.core.commands import save  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1165, in _save_cif_file  
self.save_cif_file(self._selected_model, filename)  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1177, in save_cif_file  
from chimerax.core.commands import save  
ImportError: cannot import name 'save' from 'chimerax.core.commands'
(C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\\__init__.py)  
  
ImportError: cannot import name 'save' from 'chimerax.core.commands'
(C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\\__init__.py)  
  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1177, in save_cif_file  
from chimerax.core.commands import save  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1165, in _save_cif_file  
self.save_cif_file(self._selected_model, filename)  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1177, in save_cif_file  
from chimerax.core.commands import save  
ImportError: cannot import name 'save' from 'chimerax.core.commands'
(C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\\__init__.py)  
  
ImportError: cannot import name 'save' from 'chimerax.core.commands'
(C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\\__init__.py)  
  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1177, in save_cif_file  
from chimerax.core.commands import save  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1165, in _save_cif_file  
self.save_cif_file(self._selected_model, filename)  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1177, in save_cif_file  
from chimerax.core.commands import save  
ImportError: cannot import name 'save' from 'chimerax.core.commands'
(C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\\__init__.py)  
  
ImportError: cannot import name 'save' from 'chimerax.core.commands'
(C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\\__init__.py)  
  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1177, in save_cif_file  
from chimerax.core.commands import save  
  
See log for complete Python traceback.  
  

> select clear

Traceback (most recent call last):  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1165, in _save_cif_file  
self.save_cif_file(self._selected_model, filename)  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1177, in save_cif_file  
from chimerax.core.commands import save  
ImportError: cannot import name 'save' from 'chimerax.core.commands'
(C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\\__init__.py)  
  
ImportError: cannot import name 'save' from 'chimerax.core.commands'
(C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\\__init__.py)  
  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1177, in save_cif_file  
from chimerax.core.commands import save  
  
See log for complete Python traceback.  
  

> save "C:/Users/Christl/Dropbox (UMass Medical School)/yRFC-
> building/fuck.cxs"

> hide #!1 models

> show #!1 models

> save_cif_file #1, test

Unknown command: save_cif_file #1, test  

> save_cif_file

Unknown command: save_cif_file  
Cannot determine format for '#1'  

> save test format pdb models #1

> hide #!1.1 models

> show #!1.1 models

> hide #!1 models

> show #!1 models

> hide #!1.2 models

> show #!1.2 models

> hide #1.3 models

> show #1.3 models

> hide #1.3 models

> show #1.3 models

> hide #1.3 models

> save test format pdb models #1.2

Traceback (most recent call last):  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1165, in _save_cif_file  
self.save_cif_file(self._selected_model, filename)  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1177, in save_cif_file  
from chimerax.core.commands import save  
ImportError: cannot import name 'save' from 'chimerax.core.commands'
(C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\\__init__.py)  
  
ImportError: cannot import name 'save' from 'chimerax.core.commands'
(C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\\__init__.py)  
  
File "C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 1177, in save_cif_file  
from chimerax.core.commands import save  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 376.54
OpenGL renderer: GeForce GT 730M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 20270
OS: Microsoft Windows 10 Home (Build 18362)
Memory: 8,509,480,960
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-4210U CPU @ 1.70GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (5)

comment:1 by Eric Pettersen, 5 years ago

Cc: Eric Pettersen added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: cannot import name 'save' from 'chimerax.core.commands'

comment:2 by Tristan Croll, 5 years ago

Whoops. I guess it's about time I removed that button - there's really no need for it any more, since ChimeraX's own file save interface has long-since superseded it. I'm afraid I effectively forgot it was there, which is why it hasn't been tested in a long time.

in reply to:  3 ; comment:3 by Christl.Gaubitz@…, 5 years ago 

Thanks for your quick reply, the save cmd works well. Thanks for developing ISOLDE and the new tutorial. Isolde and the tutorial are great,  I just went through it and it is really clear and well written!
Thanks, Christl

________________________________
Christl Gaubitz
Post Doc Associate Kelch Lab
http://labs.umassmed.edu/kelchlab/Lab_Website/People.html

970 LRB, 364 Plantation Street
Worcester MA, 01605
Phone
(508) 856-6868

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, August 7, 2020 1:34 PM
Cc: Gaubitz, Christl <Christl.Gaubitz@umassmed.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #3613: ISOLDE: cannot import name 'save' from 'chimerax.core.commands'

#3613: ISOLDE: cannot import name 'save' from 'chimerax.core.commands'
----------------------------------------+---------------------------
          Reporter:  christl.gaubitz@…  |      Owner:  Tristan Croll
              Type:  defect             |     Status:  assigned
          Priority:  normal             |  Milestone:
         Component:  Third Party        |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+---------------------------

Comment (by Tristan Croll):

 Whoops. I guess it's about time I removed that button - there's really no
 need for it any more, since ChimeraX's own file save interface has long-
 since superseded it. I'm afraid I effectively forgot it was there, which
 is why it hasn't been tested in a long time.

--
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ChimeraX Issue Tracker

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

Great to hear it. Thanks for the very positive feedback!

Tristan

On 2020-08-07 19:00, ChimeraX wrote:

comment:5 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed
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