How to re-define the secondary structure info in ChimeraX?
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
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
http://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html
(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.” http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin
I hope this helps, Elaine ----- 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@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
participants (2)
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Elaine Meng
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Steve Chou