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@cgl.ucsf.edu

                        http://www.cgl.ucsf.edu



On May 31, 2006, at 1:25 PM, kovzany@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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