[Chimera-users] how2 select named selections using command-line [chimera1.5.3]

[Elaine Meng]

Hi Fred,
It may be because your selection name starts with a number.  The select command may be more finicky than others because it is overloaded with two different functions, activation of models for motion (indicated by model number without #) and selection of atoms (indicated by model number with # or other specification symbol such as : for residues or @ for atoms).  Parsing the select command to try to identify the former case may interfere with recognizing your selection names.

I tried making overlapping named selections: sel1a, sel1b
and in that case you could accomplish your example with

sel sel1a & sel1b & without CA/C1'

(the last part means side chain atoms not including the CA/C1', could also use "with CA/C1' "; these are terminal entries under the Select... Structure menu, which can be used as command-line specifiers)

I personally prefer to skip selections altogether and instead use the "alias" command in a similar manner.  People may gravitate to using named selections because of Pymol terminology.   If I understand correctly, Pymol named selections are more like Chimera aliases.  For example:

alias set1 :10-20.a
alias set2 :15-35
sel set1 & set2 & ~ element.H

... see Built-In Classifications and Combinations ...
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

alias command:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>

The aliases wouldn't appear in the menu, however, except for "function" aliases as described in the documentation above.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 31, 2012, at 12:27 PM, frederick lee wrote:

> dear chimera users,
> i can defined named selections and they work under the
> select menu.
> 
> however, i canNOT use the command line to select them;
> e.g., i have 4 named selections 0a,0b,1a,1b
> 
> dis 0a | 1a works
> sel 1a NOT working
> sel :1a NOT working (said selection cleared)
> 
> i like to be able to select multiple named selections and further
> apply filters on them; e.g.,
> 
> "select 1a and 1b and atoms=side chain atoms"
> 
> how do i accomplish this? as always thank you very much.
> fred