Thanks a lot Andrea and Michael

So this would align/super impose all the other pdbs wrt the first PDB.
How Do I make a movie of that ?

Please advise
I want to be able to show this "blob" of structures(obtained after aligning) from different angles and by rotation.

I guess I would use the mset command,Would it work ?

Please also show me how to incorporate the zoom command in the python script so that the structures look well small and not enlarged and extended.



2011/7/10 Andreas Förster <>

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.


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.


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



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.

PyMOL-users mailing list (
Info Page:

       Andreas Förster, Research Associate
       Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London