[chimerax-users] How to re-define the secondary structure info in ChimeraX?

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 8 08:57:26 PST 2019

Hi Steve,
In ChimeraX, helix and strand are mutually exclusive.  You could set ss_type to the corresponding numerical value (0 coil 1 helix 2 strand).  I’ll add this information to the attributes page in the User Guide since I don’t see it there yet.

In either Chimera or ChimeraX you can leave the specification blank to mean “all” (i.e. you didn’t need the colon by itself).

There is a setattr command but slightly rearranged, so in ChimeraX it could be something like:

setattr res ss_type 0
setattr :8-12,16-21 res ss_type 2
setattr :55-61,78-92 res ss_type 1


(There should also be settable boolean attributes is_helix and is_strand but that isn’t working for me in the 2/5 daily build, and we will look into it.)

To delete element hydrogen, simply:

delete H

There is also an H atom type but element “wins.”

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

> On Feb 7, 2019, at 11:43 PM, Steve Chou <stevezchou at gmail.com> wrote:
> Dear ChimeraX developers and users,
> In Chimera, I can use the following commands to redefine the secondary structure info.
> ============================
> setattr r isHelix false :        
> setattr r isSheet false :
> setattr r isSheet true :8-12,16-21
> setattr r isHelix true :55-61,78-92
> ============================
> What's the ChimeraX equivalent?
> By the way, I can also delete the hydrogen atoms using "delete element.H" in Chimera. Is there an equivalent in ChimeraX?
> Many thanks in advance!
> Steve
> -- 
> Steve Chou

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