Re: [PyMOL] morphing between complexes

pym...@li... wrote on 11/28/2006 05:25:15 AM:

> Hi all,
> I'm new to this list and I'm a newbie of Pymol.
> I'm trying to do some morphing movies between different complexes (same
> protein but different ligands). I'm having troubles cause the morphed
> structures (pdbs generated by lsqman (procedure taken by this page
> http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html )) partially
> lost the informations about the ligands (only the core of the similar
> portion of each ligand is mantained, but the substituent are lost). Do
> you know if there is a way to solve/overcome this problem?
> Another related question is if was possible to set a ray resolution
> (let's say ray 2400, 2400) for the creation of all the frames of the
> movie (multiple png). I've been able to do that for one frame at time,
> manually...is there the possibility to set a different resolution
> recursively for all the image creation processes?
> Many thanks in advance and sorry for the long message
> Andrea
>
>

Dear Andrea -

You should try using the Gerstein Morph Server:
http://www.molmovdb.org/molmovdb/morph/

The core algorithm uses CNS, so if your structure is parsed properly by
CNS, it should emerge from the server looking OK.  You'll get a small movie
back from the server, and you can also ask it to send you the PDB files
used for each frame, so you can make your own movies in Pymol.

For making movies in complicated situations like this, I've usually used
script files to explicitly define each frame of the movie:

load file1.pdb
(rendering commands)
ray 2400,2400
png frame1.png
delete file1
load file2.pdb
etc...

You get a long script file, but you can use a text editor to copy & paste
the text blocks.

Hope that helps,

Matt

--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054



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