[Chimera-users] Creating a single pdb file from multiple pdb files

[Hurt, Darrell (NIH/NIAID) [E]]

Hi there,

I've just been doing this myself. In general, it is not a good idea to
average structures for analysis, but I'm doing it for illustrative
purposes.

I followed the lead on this page:
http://www.zelleke.com/2011/02/get-an-average-structure-from-your-trajector
y/

I use VMD to create an "averaged" structure, but the geometry of side
chains sometimes get messed up. So after doing the VMD thing, I run a
Rosetta "idealize":
http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_ide
alize.html

Once you have everything set up, the calculations take only a few minutes.

Maybe that will help someone!

Cheers,
Darrell


Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH
 
31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
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On 1/24/12 11:50 AM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

>Hi Steven,
>Sorry, currently there is nothing in Chimera to calculate average
>structures.  Chimera's "Ensemble Cluster" tool will identify clusters and
>representative structures from ensembles (where each structure has the
>same atoms, just different coordinates), but it doesn't calculate
>averaages.
>
>I was looking at the chimera-users list archive on this topic and saw
>that somebody had recommended the following:
>
><http://structbio.vanderbilt.edu/~jsmith/suppose/>
>
>I haven't tried it, however.  Best,
>Elaine
>----------
>Elaine C. Meng, Ph.D.
>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>Department of Pharmaceutical Chemistry
>University of California, San Francisco
>
>
>On Jan 24, 2012, at 3:27 AM, Steven Bottomley wrote:
>
>> Hi 
>> It is possible to create a single (preferably weighted) protein
>>structure (pdb file) from two or more related protein structures (pdb
>>files)? I guess that this would be something like creating a single
>>(weighted average) of NMR ensemble structures but using any chosen pdb
>>file. Thanks for any help!
>> Regards
>> Steven
>
>
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