[chimerax-users] assigning 3.10 helices to a pdb

[Elaine Meng]

Hi Sheena,
ChimeraX does not distinguish protein helix subtypes, they are all just "helix".  The only choices of the ss_type attribute are helix,strand,coil:

<https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>

Currently ChimeraX (and Chimera) lose some of the secondary structure information when they write out PDB files, e.g. non-alpha HELIX types, sheet membership of strands, etc.

Sorry about that.  You would have to copy the original HELIX record and use it to replace the one in the written-out file.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 3, 2021, at 3:01 PM, Sheena Vasquez <vasquezs at mit.edu> wrote:
> 
> Hi everyone,
> 
> I was wondering if there's a way to reassign alpha-helices to 3.10 helices in chimeraX? I've been using the
> setattr /A:###-### res ss_type 1 command, but it seems as if there's only the option to assign alpha helices (ss_type 1). If I try ss_type 5 (5 is the assigned number for 3.10 helices in the pdb), the helix is lost. Any help with this is greatly appreciated!
> 
> Take care,
> Sheena
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