[Chimera-users] Alignment

bodvael email bodvael at gmail.com
Tue Nov 15 12:32:11 PST 2011

Hi Elaine,

Thanks a lot for your answer, it works.

The reason I asked about the beta sheet numbers is because when I count the
number regions highlighted in green from the N-term, my stretch of amino
acids corresponds to beta sheet 7 instead of 5 (based on the original

Thus, it appears that the numbering of the beta sheets in the linear
sequence is different from their numbering in the ribbon diagram. My
question is then, what is the best way to get the numbering of the
secondary structure in the linear sequence but based on the "official"
numbering in the ribbon diagram. Else it is a bit confusing to have
different numbers for the same beta sheets.


On Tue, Nov 15, 2011 at 12:32 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> -----
> 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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