[Chimera-users] Query regarding Ksdssp assignment

Arun Prasad Pandurangan a.pandurangan at mail.cryst.bbk.ac.uk
Sun Jul 24 04:56:40 PDT 2011

Dear Eric and Elaine,

Thank you for adding the new implementation of ksdssp into the recent 
daily build. The new -v switch works fine and I am able to read the 
details of the secondary structural assignments from the reply log. For 
each residue, the reply log gives details about the helix and strand 
(ladder) assignment but not about the sheet information (i.e. to know 
which group of strands make up a sheet). I would like to know whether 
its possible to add a sheet label along with the strand assignment 
letter 'E' for each strand residues so that it will aid the 
identification of all the strands that belong to a sheet? Or to make 
things simple is it possible to add a sheet summary along with the helix 
and ladder summary in the reply log? That would be very helpful in 
annotating seconday structural assignments.

I thank Elaine, for your alternative suggestions using FindHBond tool.

Thank you.

with kind regards,
Arun Prasad

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
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> 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.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>
> Criteria:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco

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