On Mon, 14 Nov 2005, Thomas Goddard wrote:
Hi Dan,
The only model building capabilities current in Chimera are commands addaa and swapaa which add and swap amino acids, and bond rotation capabilities. We think creating capabilities for building models into density maps like the program O is too big a project. Building models without reference to maps may be easier but I suspect molecular dynamics capabilities or at least energy minimization are needed to make that useful. Chimera does not do MD calculations or energy minimization and again that is a big project we have been reluctant to take on so far.
If you think specific new model building capabilities would be helpful given the above limitations, explain them and we will be happy to consider them.
Tom
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Tom, You guys might get away with just a 'quick & dirty' energy evaluation that includes a 'soft' steric repulsive term. This could be implemented in a manner similar to the 'scuplting' feature in Pymol. Just a suggestion. This type of feature would be quite useful to our users at Vanderbilt in the Medical Center. Thanks for your consideration. Eric ______________________________________________________________________ Eric S. Dawson, Ph.D. CSB Computation, Education & Outreach Research Instructor, Biochemistry Center for Structural Biology (CSB) 5137 MRBIII Vanderbilt University