[Chimera-users] Change selection mode programatically

Mario J. Borgnia mborgnia at nih.gov
Sat Feb 7 14:12:51 PST 2015

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!


PS: The shortcuts in commands, although helpful, can be confusing. Take
"sel" in "sel sel|aromatic", it first stands for select and then for

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 at 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

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