[Chimera-users] Query regarding Ksdssp assignment

Eric Pettersen pett at cgl.ucsf.edu
Thu Jul 14 15:30:04 PDT 2011

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 Pettersen
                         UCSF Computer Graphics Lab

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