[Chimera-users] I-TASSER secondary structure

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 21 08:09:36 PST 2019

Dear Nadine,
If you sent a message earlier without membership, you would just have to wait until somebody approves it.  You did not have to become a member, you would just have to wait longer, usually just a day or two, but today is a holiday here.  :-)

About your question, you would have to look in the file yourself with a text-editor to know exactly what is in it, but if Chimera says it is using ksdssp, it means that the file did not have secondary structure assignments (lines in the PDB file starting with HELIX and SHEET).  

Our short intro to PDB format describes these lines:

I don’t know anything about I-TASSER, but probably the PDB file has just the atomic coordinates (lines that start with ATOM and HETATM).  Secondary structure assignments are different, they involve decisions of what is helix and what is beta-strand, based on calculations using the coordinates.  It is more of a “judgment call” because there are several different programs that could be used to identify secondary structure, each with adjustable parameters, so if you use a different method it might get slightly different results of where the helices and strands begin and end in the structure.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 21, 2019, at 4:12 AM, nadineh.1991 at web.de wrote:
> Dear Chimera Team,
> i just wrote you a message a few days ago without a membership. I just registered myself today and hope this message is reaching you.
> I am just writing my Master Thesis and use this wonderful program to display calculated 3D models by I-TASSER. I was wondering why Chimera is using Ksdssp algrorithm when i open these 3D models, cause i thougt the PDB files I get from I-TASSER contains these information, or am i wrong? If they do not conatin information about secondary structure what else do they contain? Only the spatial arrangement of the protein?
> Thank you for your support
> Bests, Nadine

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