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 structure. 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. Elaine 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

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