[Chimera-users] Query regarding Ksdssp assignment

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 14 15:40:52 PDT 2011

Hi Arun,
A related possibility is to use the FindHBond tool (or command) in Chimera.  Then you would get a "visual" of which strands are tied together with H-bonds into sheets.  This H-bond detection tool is completely separate from ksdssp and uses different criteria.  The resulting H-bond info (donor and acceptor atoms, distances) can be written to a file.  However, it would take a fair amount of postprocessing effort to combine this with the strand assignments to identify the sheets.



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

On Jul 14, 2011, at 3:30 PM, Eric Pettersen wrote:

> On Jul 14, 2011, at 8:52 AM, Arun Prasad Pandurangan wrote:
>> Dear Users and Developers,
>> I would like to know whether its possible to retrieve the full secondary 
>> structural assignment using Ksdssp within Chimera. For instance, I would 
>> like to know all the strands that belong to a beta sheet. If I am right, 
>> running Ksdssp from Chimera only gives details of the strand (using 
>> isStrand) and helix (using isHelix) assignment and not about sheet 
>> information. Using the full output of an another program DSSP, I am able 
>> deduce which strands belongs to which sheets. I would like to know 
>> whether similar kind of detailed output is available from Ksdssp as 
>> well. If so how to retrieve those information within Chimera?
> Hi Arun,
> 	The short answer is no.  The C++ function that does the computation does have the ability to output the same kind of summary information that the KSDSSP program itself outputs, but due to some shortcomings in Chimera's Python/C++ API interface when the function was written there is currently no way to communicate that information up to the Python layer for display.  However, between when the function was written and now we have improved that API interface and with some work it would now be possible to pass the information up and show it.  That doesn't really help you a lot right now, but I will open a feature-request ticket in Chimera's Trac database with you on the recipient list so that you will be notified when we've had time to implement it.  It may take awhile before we get to it.
> --Eric

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