Thanks to both Elaine and Darrell for your help! I also learned from the developer that Yasara Dynamics can average proteins using the AveragePos command. Regards Steven On 25/01/2012, at 1:47 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
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 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public)
Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
On 1/24/12 11:50 AM, "Elaine Meng" <meng@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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dr Steven Bottomley Unit Coordinator, and lecturer, for Biochemistry 233, Biochemistry 234, Structural Bioinformatics 332, and Molecular Techniques 632 | School of Biomedical Sciences | Faculty of Health Sciences Curtin University Tel | +61 8 9266 4369 Fax | +61 8 9266 2342 Email | mailto: s.bottomley@curtin.edu.au Web | http://curtin.edu.au [cid:b8e9ba04-1e29-4d0f-a7c1-617bc9a6e4b2@apcprd02.prod.outlook.com] Curtin University is a trademark of Curtin University of Technology. CRICOS Provider Code 00301J (WA), 02637B (NSW) This email is intended only for the use of the individual named above and may contain information that is confidential and privileged. If you are not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this email is strictly prohibited. If you have received this message in error please notify the sender immediately and delete this message. Views expressed in this message are those of the individual sender and are not necessarily the views of the Faculty of Health Science, Curtin University of Technology. Before opening any attachments please check them for viruses and defects
