[Chimera-users] MD trajectory play by commandline

[inhee park]

Dear Elaine and Eric:

Thank you for your help.
Actually the following previous posts were directly helpful to accomplish
what I wanted to do, i.e. utilizing MoveDialog.
http://www.cgl.ucsf.edu/pipermail/chimera-dev/2013/000968.html
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-August/006634.html

Now hbond information seems properly saved upon updated frame with
LoadFrame.

Thanks a lot!

#chimera --script Hbond.py
#
from chimera import runCommand
from Movie.gui import MovieDialog
from chimera.extension import manager

# pr trajectory movie open by metafile
meta = open("metafile", 'w')
meta_input = """ amber
mypdb.prmtop
pr.crd
"""
meta.write(meta_input)
meta.close()
#####
def findMDMovie():
    mdms = [inst for inst in manager.instances if isinstance(inst,
MovieDialog)]
    if not mdms:
        raise AssertionError("No MD Movie Instances!")
    return mdms[-1]
#####
runCommand("open movie:metafile; sel protein")
mdm = findMDMovie()
for x in range(1,1000+1,5):
    frame = x
    mdm.LoadFrame(x)
    runCommand("hbond selRestrict any relax true savefile hbond.%s" % x)
    runCommand("wait")
runCommand("stop") # move onto next MD trajectory


On Tue, Jan 14, 2014 at 11:06 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Inhee Park,
> A big limitation of the "coordset" command is that most formats of MD
> trajectory would have to be played through entirely using the graphical
> interface before it would work to use "coordset", as mentioned here:
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
>
> In other words, probably the frame is not updating when you use coordset.
>  Another thing that confuses me in your script is the use of "wait".  I
> don't think it is needed.  Assuming "coordset" is working, I'd use
> something like
>
> perframe myhb; coordset #0 1,1000,10
> ~perframe
>
> Sorry about that limitation.  Maybe someone else can suggest how to use
> python to play the trajectory.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> On Jan 13, 2014, at 5:18 PM, inhee park <ipark.c at gmail.com> wrote:
>
> > Dear Chimera developers and users:
> >
> >
> > I am using Chimera (production version 1.8 (build 38824) 2013-06-07
> 21:09:20 UTC).
> >
> > I wanted to process MD trajectories to extract their detailed H-bond
> information.
> > To do so, I would like to process by script with Hbond.py file.
> > $ chimera --script Hbond.py
> >
> > #---[Hbond.py]
> > from chimera import runCommand
> >
> > # pr trajectory movie
> > with open("metafile", 'w') as m:
> >     meta_input = """amber
> > mypdb.prmtop
> > pr_dry_netcdf.crd
> > """
> >     print >> m, meta_input
> > #
> > runCommand("open movie:metafile")
> > runCommand("alias ^myhb hbond relax true savefile hbond.$1")
> > runCommand("perframe myhb")
> > runCommand("coordset #0 1,1000,10; wait 100")
> > #-----------------------
> >
> > As I have many MD trajectories to be processed, I was looking for a
> commandline
> > in lieu of actually clicking buttons in MD movie GUI to play.
> > I thought that "coordset #0 1,10000,10; wait 100" may operate like
> automatically
> > starting the MD movie to load frame 1 to 1000 at every 100 interval.
> > But resulting saved H-bond files contain same information all about the
> first frame
> > (because graphically displayed was the first frame without any update
> > unless clicking the button in MD movie GUI).
> >
> > Is there a way to achieve an automatic play via commandline?
> >
> > Thank you,
> >   inhee park
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>


-- 
_________
inhee park
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