Elaine, You are great! It does help. Thanks for answering in real time. The solution that worked in my case is extending the selection by combination. I was missing the "selected" attribute in the combination, instead I was looking for some option like "append" to the select command. select #1:lys select selected|#1:arg select selected|#1:305.A and so on... Thanks again! Mario. PS: The shortcuts in commands, although helpful, can be confusing. Take "sel" in "sel sel|aromatic", it first stands for select and then for selected... On 02/07/2015 04:51 PM, Elaine Meng wrote:

Hi Mario, In command-line specifications there are operator symbols that often (but not always) allow you to specify what you want: the vertical bar “|” is for union, the ampersand “&” is for intersection, and tilde “~” is for negation. Unfortunately there are no parentheses, which can be limiting. Sometimes it also requires a bit of experimentation to verify which operations are taking priority. See “combinations” in the atom-spec docs, and also examples in the Quick Ref PDF.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/quickref.pdf>

If you are actually working with selection as opposed to simply specification, you can subtract from a selection created in an earlier command with a subsequent “~select” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html#newer>

For example, commands:

select protein & ligand z<5 ~select :trp

… would first select protein residues (amino acids) within 5 angstroms of residues classified as ligand, then deselect any tryptophans.

Further, you can add to an existing selection using the union operator, for example:

select sel | solvent

… would add all residues classified as solvent to the existing selection.

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 Feb 7, 2015, at 1:34 PM, Mario J. Borgnia <mborgnia@nih.gov> wrote:

...

Hi, I am trying to find a way to split a complex selection pattern among a number of lines in a script. I was expecting that this would be an option to the select command, but apparently it is not. I know that I can combine "select" commands by changing the selection mode to "append" in the GUI, but I am struggling to find the way of doing this from command line or from a script.

Is there a way to change the selection mode to "append" without using the GUI? Thanks Mario