match-align using just selected protein areas ?
Hello, I would like to know if it is possible in Chimera align two proteins let say protein A and protein B, but just using selected subsequences A_sel, B_sel (i.e. just the selected subsequences are going to be optimally matched and the rest of both proteins is not involved in the matching process/calculation) ? Thank you in advance ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
Hi Marek, Yes, if you mean MatchMaker (Match->Align does not align the structures, it just makes a sequence alignment from a structural alignment you already made). In the MatchMaker GUI, there is a "Further restrict matching to current selection" setting: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html> In the matchmaker (mmaker) command, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> ... it is similar but you instead specify the residues directly instead of selecting them: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 11, 2014, at 6:53 PM, Marek Maly wrote:
Hello, I would like to know if it is possible in Chimera align two proteins let say protein A and protein B, but just using selected subsequences A_sel, B_sel (i.e. just the selected subsequences are going to be optimally matched and the rest of both proteins is not involved in the matching process/calculation) ? Thank you in advance ! Best wishes, Marek
Dear Elaine, thank you very much for your help ! Best wishes, Marek Dne Wed, 12 Mar 2014 17:35:39 +0100 Elaine Meng <meng@cgl.ucsf.edu> napsal/-a:
Hi Marek, Yes, if you mean MatchMaker (Match->Align does not align the structures, it just makes a sequence alignment from a structural alignment you already made).
In the MatchMaker GUI, there is a "Further restrict matching to current selection" setting: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
In the matchmaker (mmaker) command, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> ... it is similar but you instead specify the residues directly instead of selecting them: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 11, 2014, at 6:53 PM, Marek Maly wrote:
Hello, I would like to know if it is possible in Chimera align two proteins let say protein A and protein B, but just using selected subsequences A_sel, B_sel (i.e. just the selected subsequences are going to be optimally matched and the rest of both proteins is not involved in the matching process/calculation) ? Thank you in advance ! Best wishes, Marek
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-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
participants (2)
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Elaine Meng -
Marek Maly