[Chimera-users] -S option in ksdssp command

[Eric Pettersen]

Due to a technical issue with the interface between Chimera's Python  
and C++ layers, the -S option hasn't been implemented yet.  We can  
probably get it to work with some effort, but that doesn't help you  
here.  Are you just interested in the helix/sheet assignments rather  
than the other KSDSSP info?  If so, you have a couple of options:

1) Write a PDB file (either File->Save PDB or the "write" command).   
The HELIX and SHEET records in the saved file will reflect the  
current secondary structure assignments.

2) Select helices/sheets and write the selections into files.  You  
can select helices with Select->Structure->secondary structure->helix  
or with the command "sel :/isHelix".  Selecting strands is similar.   
Save the selection to a file with Actions->Write List or with the  
"writesel" command.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu


On May 31, 2006, at 1:25 PM, kovzany at go.com wrote:

> Dear All,
>
> I'm trying to get an output with protein secondary structure
> assignment into a text file, using ksdssp command, unfortunately
> everytime I get error like this:
>
> Computing secondary structure assignments for model #0
> using ksdssp (Kabsch and Sander Define Secondary Structure
> of Proteins) with the parameters:
>   energy cutoff <default>
>   minimum helix length <default>
>   minimum strand length <default>
> -S option not yet available
>
> My question is: am I doing something wrong, or -S option is not yet
> implemented, despite it is described in ksdssp.html help file?
>
> thanks,
>
> PK
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> Chimera-users at cgl.ucsf.edu
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