[Chimera-users] MODELLER interface

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 21 09:56:12 PDT 2007

Hi Stefano,
No arguments here - we have talked about it and I've expressed a need  
for it for years.  The problem is that there are many other features  
that seem to be at least as high priority, and limited time and  
manpower available.  To name only a few of the things in progress:  
energy minimization, morphing,  interaction with dendrograms (along  
with sequence alignments), more display preferences, more animation  
commands, and producing ray-traced images.  There is a "model loops"  
tool that interfaces with MODELLER, but it only produces alternate  
conformations of loops that are already in a structure.  That was  
implemented because people in the MODELLER (Sali) group here wanted  
it the most, and it needs work - e.g. currently there is no  
convenient way to merge a chosen loop conformation back into the  

Nevertheless, this is another important item and I will share your  
message to help ensure it does not fall off "the list."  I imagine  
any validation tools would be farther down on the list than the  
interface for comparative modeling, although we do already have a  
tool that finds clashes and close contacts.

On Mar 20, 2007, at 10:05 PM, Stefano Ciurli wrote:

> Elaine,
> following our discussion on Chimera and DelPhi, and these recent  
> mails on modeling, don't you think that it would be nice to  
> interface Chimera to Modeller, as the latter one is one of the most  
> used software to do homolog modeling? The interface could be a sort  
> of way to funnel into Modeller the alignment and the structure of  
> the template(s) for Modeller to use and then read back into Chimera  
> the results of the modeling, with tools to establish the quality of  
> the model itself (I am thinking of Prosa, Procheck or WHATIF)
> Regards
> Stefano
> -- 
> ____________________________________________
> Stefano Ciurli
> Professor of Chemistry
> Laboratory of Bioinorganic Chemistry
> Department of Agro-Environmental Science and Technology
> University of Bologna
> Viale Giuseppe Fanin, 40
> I-40127 Bologna
> Italy
> Phone:	+39-051-209-6204
> Fax: 	+39-051-209-6203
> http://www.cerm.unifi.it
> http://www.isa.unibo.it/ISA/
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> ma per seguir virtute e canoscenza"
> Dante Alighieri - Inferno - Canto XXVI
> "Ihr seid bestimmt, nicht Tieren gleich zu leben,
> Nein, Tugend zu erringen und Erkenntnis"
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