[chimerax-users] assigning protein secondary structure (helix and strand)

[Rayees Mattoo]

Great! Thanks.
"dssp" solved the problem.

Best
Rayees
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, August 17, 2022 7:11 PM
To: Rayees Mattoo <rmattoo at stanford.edu>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: assigning protein secondary structure (helix and strand)

Hi Rayees,
I don't know what kind of file you saved from Coot and opened in ChimeraX.  I'm guessing PDB.

The strand and helix assignments are taken from the SHEET and HELIX records in the input PDB file, or if the PDB file doesn't have those,  calculated automatically with "dssp" (take a look at the Log when you open the structure file, it would say if this was done).

You could try re-running the "dssp" command with different parameter values,
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/dssp.html>

or manually assign secondary structure by using the "setattr" command to assign values of the residue attribute named "ss_type" as 1 (helix) or 2 (strand) instead of 0 (coil):
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>

For example, to assign residues 10-20 of chain A as helix, command:

setattr /A:10-20 r ss_type 1

However, there is another complication.  It will still draw a thin (coil-like) connector between two residues if it thinks they are in DIFFERENT helices or strands from one another.  So you may also need to assign "ss_id" values (in addition to "ss_type") to make sure that contigous residues of the same secondary structure type are also considered to be in the SAME secondary structure segment as one another.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Aug 17, 2022, at 6:23 PM, Rayees Mattoo via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Hi Elaine,
> Thanks. That is exactly what I wanted.
> One more question. I built a model in coot and then I opened in chimeraX. The model in cartoon representation shows most of the helices and sheets as loops (snapshot attached). I was wondering if there is something wrong with my model or I need to do something in chimeraX to get the cartoon display right.
>
> Best
> Rayees

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