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<TITLE>RE: [Chimera-users] PDB morphing</TITLE>
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<P><FONT SIZE=2>we tried the one file approach, did not work out.<BR>
will try again. does it make any difference about the chain id or atom number?<BR>
<BR>
<BR>
Matthew Dougherty<BR>
713-433-3849<BR>
National Center for Macromolecular Imaging<BR>
Baylor College of Medicine/Houston Texas USA<BR>
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-----Original Message-----<BR>
From: Elaine Meng [<A HREF="mailto:meng@cgl.ucsf.edu">mailto:meng@cgl.ucsf.edu</A>]<BR>
Sent: Mon 7/28/2008 11:37 AM<BR>
To: Dougherty, Matthew T.<BR>
Cc: Cong, Yao; chimera-users@cgl.ucsf.edu<BR>
Subject: Re: [Chimera-users] PDB morphing<BR>
<BR>
Hi Matt,<BR>
Currently each input conformation for morphing can only be one model. <BR>
Chimera considers each input file to be one model (or more, if the <BR>
file contains multiple sets of coordinates delimited with MODEL/ENDMDL <BR>
records).<BR>
<BR>
Without code change, the only way I can think of is to put each entire <BR>
structure of 24 monomers in a single PDB file. This may be a pain, as <BR>
you would probably want to give each monomer a unique chain ID so that <BR>
all residues in the "model" are still uniquely identifiable by residue <BR>
number/chain ID. Then you would have one file per conformation.<BR>
<BR>
Since I haven't actually tried this, I recommend trying on a subset of <BR>
2-3 chains before going to all the trouble of putting all 24 in a <BR>
file! Maybe the others can come up with a more elegant solution.<BR>
Best,<BR>
Elaine<BR>
-----<BR>
Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu<BR>
UCSF Computer Graphics Lab and Babbitt Lab<BR>
Department of Pharmaceutical Chemistry<BR>
University of California, San Francisco<BR>
<A HREF="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</A><BR>
<BR>
On Jul 27, 2008, at 8:13 PM, Dougherty, Matthew T. wrote:<BR>
<BR>
> I have a complex structure in two conformations: resting and active.<BR>
><BR>
> Each structure consists of 24 monomers, corresponding to 24 pdb files.<BR>
><BR>
> Each monomer file between conformations matches in terms of atom <BR>
> numbers, chain ID, etc.<BR>
><BR>
> I can morph a single monomer between conformations.<BR>
><BR>
> I am having no success morphing all the monomers simultaneously <BR>
> between the conformations.<BR>
><BR>
> Any suggestions on how to organize my data to overcome this?<BR>
><BR>
> thanks, Matt<BR>
><BR>
<BR>
<BR>
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