[Chimera-users] Chimera commands to record MD movies

psu4 at uic.edu psu4 at uic.edu
Thu Oct 10 17:41:14 PDT 2013


Dear Elaine and Eric,

   Really appreciate your kind help!  Sorry for the late reply.  We were
busy on the other project.

   Our volunteer Kevin modified Eric's python script.   Then we execute the
remote headless Chimera <http://www.cgl.ucsf.edu/chimera/download.html> by
the command "chimera", and "open recoding_movie_kevin.py"

*The following error message will pop out*   :

> open /work/02444/drugsu/recoding_movie_kevin.py
Executing /work/02444/drugsu/recoding_movie_kevin.py...
Reading Amber prmtop
Done reading Amber prmtop
Creating interface
Creating bonds
Bonds created
Assigning chain ID A to 259 residues, e.g. GLY
Model 2 (AAA_with_AAA_91_12A_prod_v0_l1.mdcrd) appears to be a protein
without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.

Computing secondary structure assignments...
Computed secondary structure assignments (see reply log)
Interface created

Traceback (most recent call last):
  File "/work/02444/drugsu/chimera_headless/share/ReadStdin/__init__.py",
line 79, in _runCommand
    chimera.runCommand(cmd)
  File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py",
line 2608, in runCommand
    makeCommand(*args, **kw)
  File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py",
line 69, in makeCommand
    f(c, args)
  File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py",
line 1570, in doOpen
    modelArg, noprefs)
  File "<string>", line 1, in <module>
  File "/work/02444/drugsu/chimera_headless/share/Midas/__init__.py", line
2090, in open
    noprefs=noprefs)
  File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py",
line 1817, in open
    models = func(filename, *args, **kw)
  File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py",
line 1196, in _openPython
    loadFunc(sandboxName, fileName, f)
  File "recoding_movie_kevin.py", line 39, in <module>
    runCommand('preset apply pub 1')
  File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py",
line 2608, in runCommand
    makeCommand(*args, **kw)
  File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py",
line 69, in makeCommand
    f(c, args)
  File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py",
line 1676, in doPreset
    mgr.applyPreset(type, vals[1])
  File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line
107, in applyPreset
    func()
  File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line
36, in <lambda>
    lambda:preset(publication=True, depthCued=False), False)
  File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line
183, in preset
    with nested(NA.blockUpdates(), chimera.update.blockFrameUpdates()):
AttributeError: 'module' object has no attribute 'update'

AttributeError: 'module' object has no attribute 'update'

  File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line
183, in preset
    with nested(NA.blockUpdates(), chimera.update.blockFrameUpdates()):

See reply log for Python traceback.

 If we use the GUI chimera and open this script, it will work properly.
We have searched the mailing list but didn't see similar error messages.
If not too much asking, could you kindly offer some solutions?    Please
forgive any ignorance, if any.

  Cheers,
  Pin-Chih


On Wed, Sep 18, 2013 at 4:23 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> On Sep 18, 2013, at 12:11 PM, psu4 at uic.edu wrote:
>
> > Dear Chimera,
> >
> >     Since we run a lot of Amber MD simulation in remote clusters,  we
> wonder if there is any Chimera command that can record the Amber MD
> trajectories remotely and save them as avi (or any other movie file
> formats)?   If this is feasible, then we don't have to download all the
> trajectories to local and make the trajectory movies manually.    We have
> searched the Chimera user manual but didn't see any command.   If there are
> related commands which we didn't see, please forgive us : )   Thanks.
> >
> >    * There is a way to activate X11 forwarding and use remote Chimera
> GUI to do this, but it's extremely slow and prone to freeze the computer.
>
> Hi Henry,
>         The trick is to get the trajectory loaded without using the
> graphical user interface.  When dinosaurs roamed the earth and the MD Movie
> tool was being designed, we didn't recognize the importance of providing
> command-line versions of all important functions and therefore the MD Movie
> is very much unfriendly to non-GUI usage like what you are trying to do.
>  Nonetheless, in Python almost anything is possible and indeed non-GUI
> loading of trajectories is possible using a short Python script.  I've
> attached such a script.  You would need to edit the second line of the
> script to specify where the topology and coordinate files are.  Then you
> can run it simply by opening it with the "open"command.
>         The other trick is that you will need to get the "headless"
> version of Chimera from the download page in order to be able to save
> images/movies without using the GUI.
>         Let me know if you run into any problems.
>
> --Eric
>
>
>


-- 

Pin-Chih Su (Henry Su)

Ph.D. canditate

Center for Pharmaceutical Biotechnology (MC 870)

College of Pharmacy, University of Illinois at Chicago

900 South Ashland Avenue, Room 1052

Chicago, IL 60607-7173

office      312-996-5388

fax         312-413-9303
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