Hi Bryan, Several pairs of natural protein structures appear to be related by circular permutation (and many sets have been generated by artificial means). Since these relationships are known to exist, without specifying the mechanism, it is useful for various programs to handle the situation. However, you are correct: gene duplication is one of the processes that might yield circularly permuted proteins. However, it is not the only possibility. Two proteins related by circular permutation might have been generated by fusions of two smaller parts that fused in the opposite order, for example. Here are some reviews: Uliel S, Fliess A, Unger R. Naturally occurring circular permutations in proteins. Protein Eng. 2001 Aug;14(8):533-42. http://peds.oupjournals.org/cgi/content/full/14/8/533 Russell RB, Ponting CP. Protein fold irregularities that hinder sequence analysis. Curr Opin Struct Biol. 1998 Jun;8(3):364-71. http://www.ncbi.nlm.nih.gov/entrez/ query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9666333 I hope this helps, 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 Wednesday, May 4, 2005, at 11:23 AM, Bryan W. Lepore wrote:

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

-bryan _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

On Wednesday, May 4, 2005, at 01:12 PM, Bryan W. Lepore wrote:

by the way, is the sequence alignment widget inacessible when doing e.g.

chimera --nogui cmd:input.dat

(contents of input.dat):

mmaker #0:.b #1:.a alg sw pair bb show true ^^^^^^^^^ ||||||||| N.B.

in other words, does mmaker have a keyword to specify an alignment output?

-bryan

Hi Bryan, The "show" keyword specifies that the alignment should be shown with Multalign Viewer, but there is no keyword that says a file should be written out. When you are doing things interactively, you can then use File...Save As (in the Multalign Viewer menu) to save a file. However, in your case it is the python script from Eric that tells chimera to save a file. You probably saw this already, but here is the mmaker man page listing the keywords: http://www.cgl.ucsf.edu/chimera/1.2065/docs/UsersGuide/midas/mmaker.html Not sure I'm answering your question, though... Elaine

oops - indeed Eric has addressed my question 3 days ago. sorry. 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

On Wed, 4 May 2005, Eric Pettersen wrote:

Due to the problems we are having with Chimera on Tiger we might be

didn't we all know that was going to happen? ;^) seriously, i'm sticking with Panther unless i drop my laptop in the ocean.

working, so an absolute best case would be a month and a half, and more

ok, cool with me!

likely 2-3 months. If you want the MatchMaker that considers secondary structure in the match, I have that done for the Needleman-Wunsch case and could send you the files involved. They are all Python files so they can

i'd love to try those out. -bryan