You can also do this locally on your own machine if you arrange to get the CNS morph_dist.inp script. (You need CNS to run it, of course.) The nice thing about this method is that it minimizes the structures of the intermediate morphs into something sensible. I don't know how sophisticated PyMols morphing command is, but some morphing programs simply do a linear interpolation between the starting and ending states, and that will lead to serious distortion of side chain and main chain geometries. The CNS morphing script will sort these out. The final morph, while not rigorously computed pathway between state 1 and state 2, is nevertheless a useful and possibly realistic pathway between states.

The general steps to do this are:
  1. Align the PDBs of the 2 states with your favorite software (Pymol "super" works OK), otherwise morph will include both translation and rotation
  2. PDBs must have the same exact sequence homology: edit mutations to match WT
  3. Run PDBs through a program to renumber atoms and residues. Both Res# and Atom# must begin with 1
  4. Edit the CNS morph script for initial, final PDBs and # output frames
  5. Run CNS script
  6. Load PDBs into pymol and make your movie (creates list of PNG files)
  7. Use ImageMagick to convert and animate a GIF. You can add introductory frames to the beginning and post-transformation frames at the end using ImageMagick.
Maybe there is an easier way now but this is how I have done it before.

Cheers,

_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowlett@colgate.edu

On 4/9/2014 12:45 PM, Schubert, Carsten [JRDUS] wrote:

Alternatively you could try the Morph server in Gerstein’s lab and then load each intermediate structure into a separate state for animation purposes.

 

http://morph2.molmovdb.org/

 

HTH

 

                Carsten

 

From: Sampson, Jared [mailto:Jared.Sampson@nyumc.org]
Sent: Wednesday, April 09, 2014 12:34 PM
To: sunyeping
Cc: pymol-users
Subject: Re: [PyMOL] animation showing conformational change

 

Hi Yeping -

 

With incentive PyMOL version 1.6 or later, you can use `morph`.  >From what I read at http://pymolwiki.org/index.php/Morph, you’ll need to put both conformations of the protein into one object, as different states.  See http://pymolwiki.org/index.php/Load for more info on that.

 

Cheers,

Jared

 

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/




 

On Apr 9, 2014, at 11:58 AM, sunyeping <sunyeping@aliyun.com> wrote:



Dear all,

 

If I have the structures representing two conformations of one protein, then could I make a animation movie that shows how the protein transforms from one conformation to the other conformation using pymol? Thanks.

 

 

Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

 

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