[Chimera-users] help

chinmaya joshi jchinu2014 at gmail.com
Sat Jun 11 12:34:00 PDT 2011


Hello Elaine,

Thanks a lot for your mail. I am working on the points you have suggested.
However I am a bit confused whether my input files will work in chimera or
not?
Herewith I am attaching a sample example of the  dataset which I will be
taking as the input, perform some viewpoint operation on it and then make a
movie.
Can you please let me know whether this can be done in chimera or not?
If yes, can it be done in a python script file?

Regards,
Chinmaya Joshi

On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Chinmaya,
> Before you start scripting, the first thing to consider is whether Chimera
> can do what you want.  Have you tried doing what you want to show in the
> movie, but while using Chimera interactively?  From your description, I am
> concerned that Chimera may not read your input format.  The input types are
> generally 3D data files, not images.  The one exception is that an image
> stack can be used as a "volume data" input format.  Here is information on
> what formats Chimera can read:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
>
> If you think Chimera can do what you want, here is information on making
> movies,
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html>
>
> ...including commands for rotation and translation, etc.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands
> >
>
> ...and example scripts
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples>
>
> ...however, these examples are Chimera command scripts, not python scripts.
> I think python scripts would be more difficult to make than Chimera command
> scripts, and you would only start working with python if (A) Chimera can do
> what you want or nearly so, but (B) there are no Chimera commands for those
> things.  After you figure out what you want to do by using Chimera
> interactively, then figure out the commands for those actions, then put them
> into a script.  The last step would be to add movie recording commands to
> that script.
>
> I don't know python, so I can't say any more about using that approach.
>
> I hope this helps,
> 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 Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote:
>
> > Hello,
> > I want to write a script in python to open a set of images in chimera set
> a viewpoint(rotate, translate,etc). and make a movie out of them all through
> command line for my project.
> >
> > Can someone please let me know how it can be done.
> >
> > I am new to python.
> >
> > Can anyone tell me any good links for these?
> >
> > The documentation on chimera ucsf is a bit confusing.
> > Thanks.
> > Chinmaya
>
>
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