Dear Staff -- I am interested in using Chimera but have a question regarding its use. I am interested in looking at the shape of small polypeptides --usually ranging from 5-20 amino acids -- does this program allow me to input amino acid sequences and then look at confirmational shapes? make substitutions and then compare confirmational shapes? Does the proprietary nature of my work prohibit me from using Chimera? Sincerely, Dr Scoville
Dear Dr. Scoville, (I changed the subject line because “question” is not useful to people searching for a topic)
You can build peptides, but it will not do conformational analysis for you. I.e. you would get “a” shape but Chimera wouldn’t automatically figure out the range of possible shapes (since peptides are quite flexible) or which shapes would predominate.
Besides peptide building, there is general structural analysis: you can rotate bonds, measure distances, show molecular surface, measure surface area and enclosed volume, etc. There is a full user manual with tutorials, http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/index.html http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html ...and you can search for terms of interest with the menu: Help… Search Documentation.
Chimera is free for noncommercial use. For commercial use, contact chimera@cgl.ucsf.edu Licensing: http://www.rbvi.ucsf.edu/chimera/docs/licensing.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2019, at 3:28 PM, Craig Scoville cdscoville@yahoo.com wrote:
Dear Staff -- I am interested in using Chimera but have a question regarding its use. I am interested in looking at the shape of small polypeptides --usually ranging from 5-20 amino acids -- does this program allow me to input amino acid sequences and then look at confirmational shapes? make substitutions and then compare confirmational shapes? Does the proprietary nature of my work prohibit me from using Chimera? Sincerely, Dr Scoville
Thank you for your response -- Sincerely, Craig Scoville
On Thursday, January 31, 2019, 11:02:37 AM MST, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Dr. Scoville, (I changed the subject line because “question” is not useful to people searching for a topic)
You can build peptides, but it will not do conformational analysis for you. I.e. you would get “a” shape but Chimera wouldn’t automatically figure out the range of possible shapes (since peptides are quite flexible) or which shapes would predominate.
Besides peptide building, there is general structural analysis: you can rotate bonds, measure distances, show molecular surface, measure surface area and enclosed volume, etc. There is a full user manual with tutorials, http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/index.html http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html ...and you can search for terms of interest with the menu: Help… Search Documentation.
Chimera is free for noncommercial use. For commercial use, contact chimera@cgl.ucsf.edu Licensing: http://www.rbvi.ucsf.edu/chimera/docs/licensing.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2019, at 3:28 PM, Craig Scoville cdscoville@yahoo.com wrote:
Dear Staff -- I am interested in using Chimera but have a question regarding its use. I am interested in looking at the shape of small polypeptides --usually ranging from 5-20 amino acids -- does this program allow me to input amino acid sequences and then look at confirmational shapes? make substitutions and then compare confirmational shapes? Does the proprietary nature of my work prohibit me from using Chimera? Sincerely, Dr Scoville
participants (2)
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Craig Scoville -
Elaine Meng