[Chimera-users] Alignment

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 15 09:32:46 PST 2011

Thanks Suda!

Hi Bodvael,
I would only add: 

(A) To get strand number, it is probably best to do what Suda suggested:  if looking at the sequence, just count the strands (green boxes) from N to C, or if looking at the structure, follow the ribbon from N to C.  It may help to rainbow-color the structure, which by default goes from blue at the C-term to red at the N-term (Tools... Depiction... Rainbow in the menu, or command rainbow.

Currently in Chimera the strand numbering is not necessarily from N->C... they are numbered in order of appearance in the PDB SHEET records, and sometimes the order of the strands in a sheet is different from N->C order.  Keeping that in mind, you could select strands by number (will be shown with green highlighting on the structure) with commands, for example:

select :/ssId=1 & strand

(B) After you show the whole protein sequence as Suda said, you can search for some string of residues by choosing "Edit... Find Subsequence" from the sequence window menu.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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