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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users