MOLEonline in ChimeraX

[eackad@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-55-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.91 (2019-07-02)
Description
I downloaded the results of moleOnline (in chimera format) and tried to open them using chimeraX

Log:
UCSF ChimeraX version: 0.91 (2019-07-02)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/eddie/chimeratest.cxs

opened ChimeraX session  

> select /A

Nothing selected  

> select /B

Nothing selected  

> select /P

7814 atoms, 8008 bonds, 2 models selected  

> select /P:54-90

604 atoms, 624 bonds, 2 models selected  

> open /home/eddie/code/namd/output/p450/analysis_apo/trajs/nowatmem.pdb

Chain information for nowatmem.pdb #3  
---  
Chain | Description  
P | No description available  
  

> hide #!2 models

> close #3

> close #1

> close

> open /home/eddie/code/namd/output/p450/analysis_apo/trajs/nowatmem.pdb

Chain information for nowatmem.pdb #1  
---  
Chain | Description  
P | No description available  
  

> select /P:218-235

149 atoms, 155 bonds, 1 model selected  

> color /P:218-235 grey

> color /P:242-258

> select /P:242-258

147 atoms, 148 bonds, 1 model selected  

> style selAtoms stick

Changed 147 atom styles  

> style selAtoms stick

Changed 147 atom styles  

> color /P:242-258 violet

> hide selAtoms

> save session /home/eddie/code/namd/output/p450/p450_Nussinov.cxs

> open /home/eddie/Downloads/mole_channels_oM5GDAPAYkqzANZqXz7qOw_4_chimera.py

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 582, in _qt_safe  
run(session, "open " + " ".join([quote_if_necessary(p) for p in paths]))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2646, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 616, in open  
session, filenames, format=format, name=name, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/io.py", line 479, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/io.py", line 433, in open_data  
models, status = open_func(*args, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/scripting.py", line 84, in open_python_script  
_exec_python(session, code, argv)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/scripting.py", line 59, in _exec_python  
exec(code, sandbox.__dict__)  
File "mole_channels_oM5GDAPAYkqzANZqXz7qOw_4_chimera.py", line 1, in <module>  
ModuleNotFoundError: No module named 'chimera'  
  
ModuleNotFoundError: No module named 'chimera'  
  
File "mole_channels_oM5GDAPAYkqzANZqXz7qOw_4_chimera.py", line 1, in  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 430.34
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
File attachment: mole_channels_oM5GDAPAYkqzANZqXz7qOw_4_chimera.py

mole_channels_oM5GDAPAYkqzANZqXz7qOw_4_chimera.py​

[eackad@…]

Added by email2trac

[Eric Pettersen]

Hi Eddie,

ChimeraX is not just another incremental version of Chimera, and Python scripts that run in Chimera will not run in ChimeraX, nor will command scripts -- though the commands in many cases are similar. So, the MOLEonline output designed for Chimera is only going to execute properly in Chimera, not ChimeraX -- sorry!

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[eackad@…]

Got it. I figured as much but was not sure. I really like ChimeraX. Is there any way I can open that script in chimera and export it into something ChimeraX will read?

On Wed, Aug 14, 2019 at 1:16 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:
#2314: MOLEonline in ChimeraX
----------------------------------+----------------------------
          Reporter:  eackad@…     |      Owner:  Eric Pettersen
              Type:  defect       |     Status:  closed
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:  nonchimerax  |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => closed
 * resolution:   => nonchimerax


Comment:

 Hi Eddie,
         ChimeraX is not just another incremental version of Chimera, and
 Python scripts that run in Chimera will not run in ChimeraX, nor will
 command scripts -- though the commands in many cases are similar.  So, the
 MOLEonline output designed for Chimera is only going to execute properly
 in Chimera, not ChimeraX -- sorry!

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2314#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker


--
_________________________________________________________
Edward Ackad, Ph.D<http://www.siue.edu/%7Eeackad>
Associate Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390

[Eric Pettersen]

We are working on a bare-bones Chimera → ChimeraX exporter that will be available in a month or so that won't cover nearly enough to export your MOLEonline output, but the exporter will be improved over time. Right now you could export from Chimera using COLLADA format and read that into ChimeraX. I tried it and it worked. Though they both clearly have the same geometrical objects, I might prefer the way the transparency looks in Chimera to the way it looks in ChimeraX. Nonetheless there may be other reasons you want to use ChimeraX for this, and the export/import does work.

--Eric

[eackad@…]

Awesome, thanks so much for looking into this!
One reason I love ChimeraX is the simple VR. It is so simple and so well done it feels like a completely additional tool to just being a visualization software. Truly excellent work by you guys!!
Cheers,
Eddie

On Wed, Aug 14, 2019 at 3:55 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:
#2314: MOLEonline in ChimeraX
----------------------------------+----------------------------
          Reporter:  eackad@…     |      Owner:  Eric Pettersen
              Type:  defect       |     Status:  closed
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:  nonchimerax  |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+----------------------------

Comment (by Eric Pettersen):

 We are working on a bare-bones Chimera → ChimeraX exporter that will be
 available in a month or so that won't cover nearly enough to export your
 MOLEonline output, but the exporter will be improved over time.  Right now
 you could export from Chimera using COLLADA format and read that into
 ChimeraX.  I tried it and it worked.  Though they both clearly have the
 same geometrical objects, I might prefer the way the transparency looks in
 Chimera to the way it looks in ChimeraX.  Nonetheless there may be other
 reasons you want to use ChimeraX for this, and the export/import does
 work.

 --Eric

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2314#comment:4>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker


--
_________________________________________________________
Edward Ackad, Ph.D<http://www.siue.edu/%7Eeackad>
Associate Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390

[Eric Pettersen]

Thanks!! VR has turned out to be way more useful than we thought it was going to be. The immersiveness really aids understanding of structural relationships. Glad you like it!

--Eric

[Elaine Meng]

Hi Edward,
I know it's been 3 years since this ticket was made... Just thought I would let you know that a reader for the "Json" download from MOLEonline has recently been added to ChimeraX. If you download the file blahblahblah.json and then simply open it in ChimeraX, it will show a slider for flipping through channels. You would also have to open the protein yourself separately. The channels are pseudoatomic models initially shown as partially transparent, but you can change their transparency and/or color, show more than one channel at a time, etc. Brief description of this newly supported "open" format here:
<​https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#object>

You would have to get a daily build, is not in the 1.4 release. We hope to make a 1.5 release in a few weeks, though.
Best,
Elaine