[Chimera-users] Extracting secondary structure residue info

Prathvi Singh prathvi at iitk.ac.in
Sat Apr 2 09:51:47 PDT 2022

Thanks a lot Elaine. It helped enormously. I just have 2 more questions:

1. After running the dssp command in chimeraX, is there a command to save
the reply log to file using a command? I searched for it & landed up at:
https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003739.html but
chimeraX throws the "Unknown command" error.

2. Is there a way to extract polypeptide sequence from a PDB file & save as
a FASTA file or even a simple text file which simply contains a string
representing the amino acids as single letters alphabets?

On Fri, Apr 1, 2022 at 9:15 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016
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