[Chimera-users] correction: selecting by element

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 16 09:53:52 PDT 2009

Begin forwarded message:

>> You can use all the end entries in the Select... Chemistry menu also
>> in the command line.  These symbols are in the element submenu.  In
>> cases where there is ambiguity, for example H appears both under
>> element and under IDATM type, you can disambiguate like
>> select element.H
>> It will work to use element.Mg and element.Ca ... it's just more
>> typing.
> Hum that does not seem to work oddly. "Select element.Ca" gives me a
> "mangled atom specifier" (that why I asked you in the first place).
> Same thing for Mg btw (I originally though there was some ambiguity  
> between
> Calcium and carbon-alpha naming).

Whoops, my bad.  Actually Mg and Ca are not at the top level of  
"Select... Chemistry... element" but in further submenus. You could  
use "Md-Ni.Mg" and "Be-Cl.Ca" but I don't think there is a need to use  
anything longer than Mg and Ca.  Ca will not conflict with atom name  
because the command-line syntax requires @ to indicate atom name.   
"@ca" are atoms named CA, "@c" are atoms named C, "Ca" are calcium  
ions/atoms, "C" are carbon atoms.  The capitalization is not important  
for atom names, but it IS important for the things that are also menu  
entries and should match what is shown in the menu.  The potential for  
ambiguity with element symbols is with the entries under "Select...  
Chemistry... IDATM type" but in fact H is the only one I can think of  
that appears in both places.


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