[Chimera-users] Concerns regarding secondary structure

[Elaine Meng]

Hi Rodrigo,
If a PDB file doesn't have HELIX and SHEET information in it, the ksdssp
program is used to detect the secondary structure.  Ksdssp uses the 3D
structure (it doesn't matter what the sequence is).  However, even if  
the
3D structure looks almost the same in the new model as in the original,
there are reasons the assignments might be different:

(a) the original structure has HELIX and SHEET information in it, and
the person who determined that information used a different method than
ksdssp, or different parameters

(b) the structures are slightly different, causing the strands not
to be predicted in the new structure

There are some ways you can change the HELIX and SHEET assignments if
you feel they are not right:

(a) select the residues you think should be in beta-strands, open the
Selection Inspector (click the button on the bottom right corner
of the Chimera window), Inspect "Residue", set "is strand" to "true"

(b) re-run the ksdssp algorithm but with different parameters.  Open
the Model Panel (Favorites... Model Panel), switch to the "infrequently
used" list of functions, choose "compute SS".  Try Apply-ing different
parameters.  If you want particular values of these parameters to always
be used (for any proteins without HELIX and SHEET info), you can click
"Save as Defaults"

I hope this helps,
Elaine

On Dec 8, 2005, at 4:26 PM, rquiroga at immf.uncor.edu wrote:

> Greetings,
>
> I have some concerns with Chimera's secondary structure detection/ 
> depiction.
>
> I am using Modeller to predict some 3D structures.
>
> I open my predicted structure in pdb file in Chimera along with the  
> original
> structure I based my prediction on, and find that my predicted  
> structure lacks
> two beta sheets that the model protein has, though the AA that  
> compose the
> B-sheet are identical for the two proteins when I compare sequences  
> with
> Matchmaker.
>
> I tried opening my predicted structure in MolMol and it detects the  
> B-sheet,
> though I hugely prefer Chimera, so if you could solve this problem  
> for me I
> would be very greatful.
>
> Thanks in advance, and regards
>
> Rodrigo Quiroga
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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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-----
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