[Chimera-users] Question about Labeling Beta Sheet

[Elaine Meng]

Hi Yifan,
Sorry no, Chimera (and ChimeraX) do not keep sheet information, only whether a residue is in a strand.

If you had a PDB file of a structure already deposited in the protein databank, you could use a text-editor to look in the SHEET information.  However, I'm thinking it may be your own new structure.

Some possibilities are to:

(A) display H-bonds between strands and then you can confirm which ones are tied together into a sheet

Chimera commands:
sel strand
hb selRestrict both

ChimeraX command: hbonds strand

- OR -

(B) (re)run the program that defines secondary structure DSSP in verbose mode and then see the "Ladder Summary" near the top of its output in the Reply Log.  Even the ladder summary only gives strand pairs, so you have to see whether the same residue numbers appear in different pairs which would make them in the same sheet as each other.

Chimera command: ksdssp -v
ChimeraX command: dssp report true

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

> On Dec 22, 2022, at 10:40 AM, Yifan Wang via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Chimera team,
> 
> I have a question for labeling beta sheet. After I get secondary structure, when I look at the 3D structure, It is very clear to see coli, helix and beta-strands. But how can I label and tell the beta strands are in same sheet or not? Does chimera contain the information for beta sheet? 
> 
> Thank you so much!
> Yifan