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