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<div class="PlainText">Thanks to both Elaine and Darrell for your help!<br>
<br>
I also learned from the developer that Yasara Dynamics can average proteins using the AveragePos command.<br>
<br>
Regards<br>
Steven<br>
<br>
On 25/01/2012, at 1:47 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:<br>
<br>
> Hi there,<br>
> <br>
> I've just been doing this myself. In general, it is not a good idea to<br>
> average structures for analysis, but I'm doing it for illustrative<br>
> purposes.<br>
> <br>
> I followed the lead on this page:<br>
> <a href="http://www.zelleke.com/2011/02/get-an-average-structure-from-your-trajector">
http://www.zelleke.com/2011/02/get-an-average-structure-from-your-trajector</a><br>
> y/<br>
> <br>
> I use VMD to create an "averaged" structure, but the geometry of side<br>
> chains sometimes get messed up. So after doing the VMD thing, I run a<br>
> Rosetta "idealize":<br>
> <a href="http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_ide">
http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_ide</a><br>
> alize.html<br>
> <br>
> Once you have everything set up, the calculations take only a few minutes.<br>
> <br>
> Maybe that will help someone!<br>
> <br>
> Cheers,<br>
> Darrell<br>
> <br>
> <br>
> Darrell Hurt, Ph.D.<br>
> Section Head, Computational Biology<br>
> Bioinformatics and Computational Biosciences Branch (BCBB)<br>
> OCICB/OSMO/OD/NIAID/NIH<br>
> <br>
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> On 1/24/12 11:50 AM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:<br>
> <br>
>> Hi Steven,<br>
>> Sorry, currently there is nothing in Chimera to calculate average<br>
>> structures. Chimera's "Ensemble Cluster" tool will identify clusters and<br>
>> representative structures from ensembles (where each structure has the<br>
>> same atoms, just different coordinates), but it doesn't calculate<br>
>> averaages.<br>
>> <br>
>> I was looking at the chimera-users list archive on this topic and saw<br>
>> that somebody had recommended the following:<br>
>> <br>
>> <<a href="http://structbio.vanderbilt.edu/~jsmith/suppose/">http://structbio.vanderbilt.edu/~jsmith/suppose/</a>><br>
>> <br>
>> I haven't tried it, however. Best,<br>
>> Elaine<br>
>> ----------<br>
>> Elaine C. Meng, Ph.D.<br>
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
>> Department of Pharmaceutical Chemistry<br>
>> University of California, San Francisco<br>
>> <br>
>> <br>
>> On Jan 24, 2012, at 3:27 AM, Steven Bottomley wrote:<br>
>> <br>
>>> Hi <br>
>>> It is possible to create a single (preferably weighted) protein<br>
>>> structure (pdb file) from two or more related protein structures (pdb<br>
>>> files)? I guess that this would be something like creating a single<br>
>>> (weighted average) of NMR ensemble structures but using any chosen pdb<br>
>>> file. Thanks for any help!<br>
>>> Regards<br>
>>> Steven<br>
>> <br>
>> <br>
>> _______________________________________________<br>
>> Chimera-users mailing list<br>
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> <br>
> <br>
<br>
Dr Steven Bottomley<br>
Unit Coordinator, and lecturer, for Biochemistry 233, Biochemistry 234, Structural Bioinformatics 332, and Molecular Techniques 632 | School of Biomedical Sciences | Faculty of Health Sciences
<br>
<br>
<br>
Curtin University<br>
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Fax | +61 8 9266 2342<br>
<br>
<br>
Email | mailto: s.bottomley@curtin.edu.au <br>
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<br>
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