Re: [PyMOL] animation showing conformational change

[Roger R. <rro...@co...>]

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: rro...@co...

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:Jar...@ny...]
> *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 <sun...@al... 
> <mailto:sun...@al...>> 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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