hi elaine, thanks for the quick help. i tried using aliases just now. now i have 4 aliases: g0a, g0b, g1a, g1b. i can only sel all 4 groups by using
sel g0a | g0b | g1a | g1b
the & operator returns nothing as there are no intersection among the 4 groups. seemed the & is intersection and not plus here. when i used
sel g0a,g0b,g1a,g1b i got error.
given above, seemed like i need to do something like
sel (g0a | g0b | g1a | g1b) & without CA/C1' but parentheses are not legal here. how should i get around this? thanks again. fred
On 01/31/2012 12:46 PM, Elaine Meng wrote:
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