Alignment of repeated domains
Hello, I'm using the tool MatchMaker to align different structures. My reference protein has 3 domains very similar and I would like to show an alignment of other 3 proteins with each one of those 3 domains. The problem is that the 3 protein always align to the same domain (one of the 3, instead of each one with a different domain). How can I do so I can exclude the part of the protein already aligned in new alignments? I hope I explained myself and thank you in advance. Francisco Benitez.
Hello Francisco, You can specify just the part to use for the alignment. In the graphical interface (MatchMaker dialog), you would select the part of the structure you want to use and then turn on the option to "Further restrict matching to current selection,” described here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchma...> … or if using the “matchmaker” command, you could specify residue number range directly in that command to restrict the fit, as described here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict> Example: mm #0:50-100.A #1 … will only use residues 50-100 in chain A of the reference structure #0 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 26, 2018, at 12:15 PM, Benitez De La Fuente, Francisco <fran.benitez@botany.ubc.ca> wrote:
Hello, I'm using the tool MatchMaker to align different structures. My reference protein has 3 domains very similar and I would like to show an alignment of other 3 proteins with each one of those 3 domains. The problem is that the 3 protein always align to the same domain (one of the 3, instead of each one with a different domain).
How can I do so I can exclude the part of the protein already aligned in new alignments?
I hope I explained myself and thank you in advance. Francisco Benitez.
It perfectly solved my problem. Thanks so much Elaine for your help and quick answer. Have a good Friday! Francisco Benitez. ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Friday, January 26, 2018 14:49 To: Benitez De La Fuente, Francisco Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Alignment of repeated domains Hello Francisco, You can specify just the part to use for the alignment. In the graphical interface (MatchMaker dialog), you would select the part of the structure you want to use and then turn on the option to "Further restrict matching to current selection,” described here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchma...> … or if using the “matchmaker” command, you could specify residue number range directly in that command to restrict the fit, as described here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict> Example: mm #0:50-100.A #1 … will only use residues 50-100 in chain A of the reference structure #0 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 26, 2018, at 12:15 PM, Benitez De La Fuente, Francisco <fran.benitez@botany.ubc.ca> wrote:
Hello, I'm using the tool MatchMaker to align different structures. My reference protein has 3 domains very similar and I would like to show an alignment of other 3 proteins with each one of those 3 domains. The problem is that the 3 protein always align to the same domain (one of the 3, instead of each one with a different domain).
How can I do so I can exclude the part of the protein already aligned in new alignments?
I hope I explained myself and thank you in advance. Francisco Benitez.
participants (2)
-
Benitez De La Fuente, Francisco -
Elaine Meng