[Chimera-users] Extracting secondary structure residue info

[Elaine Meng]

Hi Prathvi,
When you open a protein structure file that doesn't already have HELIX and STRAND information, Chimera (and ChimeraX) automatically run a calculation to assign secondary structure.  The algorithm is the same, but in Chimera it is the "ksdssp" command and ChimeraX it is the "dssp" command.

Chimera "ksdssp" does NOT have the option, but if you open the structure in ChimeraX you can rerun the "dssp" command except with "report true" to give that information in the Log:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/dssp.html>

This ChimeraX dssp report shown in the Log starts like this and has more details  after the summaries:
----------------
Helix Summary
LEU /A:105 -> ASP /A:107
ASN /A:198 -> GLN /A:200

Ladder Summary
ASP /A:12 -> TYR /A:14 antiparallel GLY /A:44 -> LYS /A:46
GLY /A:15 -> SER /A:24 antiparallel ILE /A:331 -> PHE /A:340
[...etc.]

In Chimera, there is a way to get the information, but it is much less convenient.  You would have to save the residue attribute named isHelix to a text file, and then save the residue attribute named isStrand to another text file.  Then you would have to look in the files to identify the ranges or residue numbers.  How to save an attribute to a file is described in the bottom section of this page:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

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




> On Apr 1, 2022, at 12:18 AM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> I have a PDB file which only has rows starting with ATOM. When I open it in UCSF chimera, it displays all the secondary structures which the residues form. Is it possible to extract the starting & ending residues of each alpha helix (or any other secondary structure for that matter)?
> 
> -- 
> Prathvi Singh,
> Research Fellow,
> Department of Biological Sciences & Bioengineering,
> Indian Institute of Technology, Kanpur-208016
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