Hi, I solve comparable problems as follows: First I store the new trimer in Chimera as a single pdb file, but it would open as three sub-files which is not accepted by Modeler as template. I open the pdb file in a text editor and delete the "model 1", "model 2" etc lines als well as the "ENDMDL" lines from the pdb text file, in order to obtain a pdb file of the trimer that opens in Chimera as a true single file. I use this new pdb file of the trimer as template to remodel (in Modeller) the sequence of the trimer (i.e. the three consecutive sequences of the monomers). In the resulting homology model, all secondary structures are unchanged, but the loops at the interfaces do not overlap any more, because Modeller prevents this. Of course the true conformation of these loops remaines unknown. However, we use such molecular models for fitting them into cryoEM densities, and the latter hopefully give us information about the shape of the loop. Best regards Juergen ________________________________________ Von: chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu] im Auftrag von Elaine Meng [meng@cgl.ucsf.edu] Gesendet: Freitag, 19. März 2010 18:58 An: akshita kumar Cc: chimera-users@cgl.ucsf.edu Betreff: Re: [Chimera-users] Dimer construction from a monomer generated using Modeller Dear Akshita, I don't think this is something you can handle effectively with Chimera. Instead, it might be possible to: (a) from the trimer of the model you have now, re-model just the loops using Modeller so they don't conflict with each other - OR - (b) instead of modeling a monomer from the template monomer, use Modeller to model a trimer starting from a template trimer, which might also the loops more sensibly However, I don't know either of these things can be done, or how to do them, since I don't have direct experience. You might try asking on the Modeller forum: <http://salilab.org/modeller/discussion_forum.html> Good luck, 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 Mar 19, 2010, at 3:33 AM, akshita kumar wrote:

Dear Members,

Using 1T3D as template, we have generated a homology model via Modeller. As the biological unit is a trimeric structure we need to generate trimer of the model too. Therefore we undertook structural alignment of the model and individual template 1T3D chains ("a, b , c"). However in our model the loop region that falls at the interface between two dimers is much longer and as a result the loops between dimer overlap each other.

Can anybody please suggest a solution for generating a dimer/trimer from the monomer built using homology modelling.

Thanks Akshita

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Hi Forbes, I'm hoping others will pipe up, since I don't have wonderful answers... I'm not aware of any work on directly interfacing either Delaunay tessellation or elastic network model calculations with Chimera. For Delaunay tessellation, Qhull is freeware, and I even thought we were using it for something in Chimera, but I don't think it is in python. <http://wareseeker.com/Home-Education/qhull-2010.1.zip/370b017fb> Chimera does connect to the NIH Structools server to get atom- associated Voronoi volumes assigned as attributes (see Tools... Surface/Binding Analysis... Area/Volume from Web), but there is no display of the actual tessellation. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.htm...

The CASTp pocket area/volume information that can be shown in Chimera is calculated using the weighted Delaunay triangulation, but you only get the results, again not the tessellation. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html> For ENM and similar, there are a number of web servers, but they do not provide output convenient for viewing in Chimera. Here are a few (and surely there are more): elNemo elastic network model server <http://www.igs.cnrs-mrs.fr/elnemo/start.html> AD-ENM web server <http://enm.lobos.nih.gov/> Anisotropic Network Model web server <http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi> 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 Mar 23, 2010, at 10:32 AM, Forbes J. Burkowski wrote:

Hi: Do you folks know if there is a Python Script to do Delaunay Tessellation for proteins?

I am also wondering if anyone has written code to handle Elastic Normal Mode analysis.

Any suggestions or pointers would be appreciated. Many thanks, Forbes Burkowski

Hi Forbes, The Chimera Intersurf tool uses Delaunay tessellation and the Python code is the ComputeTetrahedralization() function in file chimera/share/Intersurf/SurfMaker.py It uses the third-party Qhull package included with Chimera. The AIRS package of Chimera extensions that come with EMAN (single particle EM reconstruction code) includes a tool called ModeViewer that computes normal modes using MMTK. I do not see any documentation for it. I did try it long ago and it worked. http://ncmi.bcm.tmc.edu/software/AIRS Tom

Hi:

Do you folks know if there is a Python Script to do Delaunay Tessellation for proteins?

I am also wondering if anyone has written code to handle Elastic Normal Mode analysis.

Any suggestions or pointers would be appreciated.

Many thanks,

Forbes Burkowski

Hi: WOW! Thanks for all the leads. I will look into these. Cheers, Forbes On Tue, 23 Mar 2010, Elaine Meng wrote:

There's a server for that too (normal modes via MMTK)!

WEBnm <http://services.cbu.uib.no/tools/normalmodes>

Elaine

On Mar 23, 2010, at 11:55 AM, Thomas Goddard wrote:

...

computes normal modes using MMTK.