These are not Chimera questions but general modeling questions. I would suggest - reading papers where similar modeling is done, to see what procedures they use - finding a textbook or online courses on homology modeling - talking to others who do this type of modeling You could try asking questions on ccl.net -- however, you will probably need to spend some time learning about the problem yourself because the exact answer will depend on your structure and what you want to use it for, and only with understanding can you make the proper decision. My general advice is that simple minimization often cannot provide a good structure. For homology modeling in general (not just a few mutations), other programs are currently better than Chimera. I thought swissmodel already made the homology model for you. There is also the modeller program, or databases such as modbase that have homology models already made. See these previous messages for more discussion: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-March/001420.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-January/002202.html

Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 15, 2009, at 12:37 AM, gytjyb wrote:

Thank you very much for you answer. My english is not very well,Because I just come from china. My major subject is gene structure,So I am not good at protein structure. But ,I think this is very useful for me to analyze protein structure and asure their structure. So,I must thank for you first! You means: If I get a homologous model structure from swissmodel which I just align with PDB stucture,i must minimize structure ,at first。 But before i do minimization,I should add water or not.so this is a question.Which condition should I add water? Secondly,I get a stable structure after minimization.If I want to do mutation, I should do minimization for every time mutation about this structure. Thank you very much! Thank you very much! BEST WISHES FOR YOU!