May 2005 - Chimera-users - RBVI Mailing Lists

beta version of Sequence.py
by Bryan W. Lepore 05 May '05

05 May '05

i'm trying out the secondary structure matching stuff that Eric wrote, and i'm wondering if there is a updated Sequence.py package (that has the StructureSequence functions)? b/c the new MatchMaker/__init__.py trys to import StructureSequence, but its not in chimera/Sequence.py. -bryan

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os x tiger
by Grant Geske 04 May '05

04 May '05

has anyone tried running chimera on the new mac os tiger?? i did and it did not work. does anyone have any suggestions?? grant ________________________________ Grant Geske Blackwell Group University of Wisconsin-Chemistry 1101 University Ave Madison, WI 53706 PH: 608-262-9043 email: chemg(a)mac.com

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circular permuation
by Bryan W. Lepore 04 May '05

04 May '05

i want to test my understanding about the "circular permuation" during matching: is this for proteins that result from gene duplication? -bryan

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Fwd: [Chimera-users] writing alignment
by Elaine Meng 04 May '05

04 May '05

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: Wed May 4, 2005 1:56:54 PM US/Pacific > To: "Bryan W. Lepore" <lepore(a)brandeis.edu> > Subject: Re: [Chimera-users] writing alignment > > > On Wednesday, May 4, 2005, at 01:41 PM, Bryan W. Lepore wrote: >> however i'd like to ask if mmaker is in fact not written to handle >> specific stretches of a model - e.g you can do #1:.a at the least? >> e.g., not something like #1:.a1-10,a15-20... to prune out areas to >> ignore. >> >> -bryan >> > > Hi Brian, > You can specify which chains (like in that example you included > in a previous mail) to construct an alignment with, but not > subparts of those chains. > > However, remember that the structure matching will only use > residues that are actually aligned in the initial sequence alignment. > So, it doesn't matter if the sequences have other parts > that are essentially unalignable. > Elaine >

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mmaker
by Bryan W. Lepore 03 May '05

03 May '05

i'm confused about the command "mmaker". `chimera --nogui mmaker` causes a "no such file or directory" error, so i tried `chimera --nogui --mmaker` which isnt' right either. also tried just `mmaker` even though its not in bin/ lib/. so do i make a heredoc script? i suspect i am missing a fundamental point (that i didn't find with `google: mmaker site:www.cgl.ucsf.edu/chimera`). i've tried both the latest official release and the lastest snapshot. -bryan

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by Ihms, Elihu C 02 May '05

02 May '05

I noted that Apple still has X11 availible for download, just that it's not publicized. http://a1408.g.akamai.net/7/1408/1388/20030317/akamai.info.apple.com/X11/us… Keep up the good work on Chimera! -- Elihu Ihms [ ihms(a)tamu.edu ]

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Chimera-users May 2005