[Chimera-users] Sec structure loss

[Elaine Meng]

Hi James,
There are many different secondary structure assignment methods (and  
sets of parameters), and they often disagree to various extents.   If  
the PDB file has HELIX and SHEET information in it, that will be  
used.  Take a look in the files - if they do have such information,  
it comes from the depositor, and different depositors have used  
different methods.

If files do not have that information, Chimera will perform an  
assignment.  Chimera uses "ksdssp" and there is no other choice of  
method, but you can adjust the parameters that it uses by default by  
choosing "compute SS" from the Model Panel, see:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ 
modelpanel.html#computess
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html

Also by default, MatchMaker runs "ksdssp" - it uses both sequence and  
secondary structure information to align structures, and we found it  
tends to improve the superpositions when a consistent secondary  
structure assignment method is used on all the structures being  
aligned.  Nevertheless, you can turn off the option to run "ksdssp"  
beforehand.  (Need to re-open the structure files to get back their  
original assignments, however.)

There is no real gold standard of what is a helix and what is a  
strand.  There is no problem when the structure is nearly ideal, only  
as it becomes less regular or shorter.   Thus it is hard to say  
something is definitely wrong.  However, if to your eye you would  
prefer something to be assigned as a strand, you can just set it  
manually with Selection Inspector or "setattr" as described here:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-August/001775.html

To display both backbone atoms and ribbon, use the command  
"ribbackbone" - it may not look very good, however, as the ribbon is  
a smoothed interpolation... the atoms may not fall right on top of  
the ribbon in some places.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at 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 May 2, 2008, at 2:19 PM, James Fethiere wrote:

> Hi,
> I'm seing something strange with secondary structure assignments in  
> peptides. Two examples: PDB 1axc has a peptide bound to PCNA with  
> beta strand interactions and chimera doesn't pick it up as a  
> strand. In the other example, 1rxz, it picks up the strand in a  
> similar peptide but the strand disappear when I run matchmaker with  
> 1ul1 (which also has a strand at the c-terminus that is not picked  
> up. Is there any explanation? Are the criteria for secondary  
> structure assignments to strict?
>
> One more thing that may have been asked already!!  how does one  
> keeps the NH and CO of the peptide bond displayed in the ribbons view?
> Thanks
> James
>



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