[Chimera-users] beta sheet to loop

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 19 10:23:53 PST 2017


Hi Jiri,
Different methods of calculating secondary structure use different criteria and/or cutoffs, and it is very common that they will produce different results in some places.  If the PDB file had HELIX and SHEET information in it, then Chimera is just showing that.  If the PDB file didn’t have such information, Chimera will try to calculate it using its built-in “ksdssp” method.  However, you can always re-run “ksdssp” (it is a command too) with different parameters, or if you know exactly what you want some residue to be (helix, strand, or neither), you can assign it directly.

ksdssp command:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>

To change the assignment directly, select the residues of interest using whatever method you prefer (mouse, Sequence window, etc.) and then use either the Selection Inspector or the “setattr” command.

Selection Inspector method: 
Click the green magnifying glass icon near the bottom right of the Chimera window to show the Selection Inspector, inspect: Residue, and then change the values for “in helix” and “in strand” as you prefer, as long as only one of them (or neither) is set to “true”.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>

Command method would be something like:
setattr r isStrand true sel
setattr r isHelix false sel

Or, instead of “sel” you could specify the residues directly, and then you wouldn’t need to select them first, e.g. “setattr r isStrand true #0:12-14.A”.  Just remember to avoid setting any residues as both helix and strand.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

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

> On Jan 19, 2017, at 6:51 AM, chemocev marker <jirivitali at gmail.com> wrote:
> 
> Hi
> I am looking at some region of the protein in chimera and it looks like a loop but the from the procheck analysis it shows a beta-hair pin like structure. In the electron density, its shows a hydrogen bonding between the main chain atom. Why is this difference and how to overcome on it.
> best
> Jiri 




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