using pymol for making movie of change in protein structure

From: sonali dhindwal
Date: 21 March 2012 14:52

Dear All, My query is slightly out of scope of ccp4. I need some suggestions for making movie using pymol to show conformation of a reactive site loop, through the use of three crystal structure which are available showing this change. I have seen many people present the structural information in the form of movie, to show how the ligands come and the flexible residues  moves giving change in the active site by movement of the flexible loops.  I found emovie and installed the plugin but  pymol installed on my system doesnt support the morph feature. Can someone please help in suggesting some other tool and tutorial for the same. Thanks in advance. Regards

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From: Bosch, Juergen

you can use moleman2 to generate intermediates between your three xtal structures and morph them. Check out the manual on the USF pages, it's very straightforward. Or you can use the Morph server http://www.molmovdb.org/molmovdb/morph/

Jürgen

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From: Ed Pozharski


This may be useful

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera
http://pymol.sourceforge.net/newman/user/S0300movies.html

--
"I'd jump in myself, if I weren't so good at whistling."
                              Julian, King of Lemurs

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From: Federico Forneris


Hi,
A quick and efficient option for morphing between multiple states (structure
A --> structure B) defined by separate PDB structures is using UCSF chimera.
The program will generate a user-defined number of intermediate pdb models
that can be saved and used in Pymol.

Best,

Federico Forneris, PhD

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From: Randy Read

You've already had an answer about the morphing part of the question, so I'll just address the question about tools.

In terms of making a movie, if you aren't already an expert in making movies with PyMol, I'd suggest starting first with ccp4mg.  Once you have a set of coordinate files for the morph, it's very easy to make a nice movie.

Best wishes,

Randy Read

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From: Alan Cheung


And UCSF Chimera works very well too - their website has loads of examples.


Alan

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From: sonali dhindwal

Dear All, Thanks a lot to all, for replying to my query. and yes Dr. Read, i m trying to make the movie for the first time but hopefully with the help of CCP4bb, i will be able to do the task. Thanks again. Regards -- Sonali Dhindwal "Live as if you were to die tomorrow. Learn as if you were to live forever."