Just a little bit of a further note on top of what Andreas said. If you are doing all of the commands from a script you might want to cmd.disable() the first molecule so that you can align to it, but not see it in the animation.  Then you can delete each molecule (after 1) after you've used it.

2011/7/10 Andreas Förster <docandreas@gmail.com>
Holfelder!

I don't see your doubts.  Your first point's a guess - and you're right
- and the second one a questions.

Before I answer, one warning:  If you have 10000 pdb files and numbering
starts at 1, the last one will be 10000, not 9999 like you say.  Be
aware of what you have.

for i in range (1,10001): \
  cmd.load("x_%d.pdb" %i) \
  cmd.super("x_%d" %i, "x_1")

Will load 10000 files and superpose every structure onto the first.  The
curious % notation substitutes a variable into a string.  The load loads
files and super superposes one structure onto another.

Hope that helps.


Andreas



On 10/07/2011 12:05, Babban Mia wrote:
> Hello Everyone
>
> I have got a doubt relating to making PYMOL MOVIE.
> I have like 10,000 PDBs named x_1.pdb .....x_23.pdb and so on
>
> I want to make a movie which essentially should act as the slideshow
> from x_1.pdb to ..... x_9999.pdb
>
> This would show,kind of show the MD simulations for the protein.
>
> DOUBTS :
>
> 1 . I guess I would have to align the pdbs wrt some source to actually
> be able to see the real MD changes in the succeeding pdb structures.
> 2. Please show me some commands on how I can achieve all of above.
>
> Thanks again
>
> Best
>
> Holfelder
>
>
>
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--
        Andreas Förster, Research Associate
        Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
            http://www.msf.bio.ic.ac.uk

------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
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Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University