[Chimera-users] explicit parentheses in atom selections

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 2 08:48:53 PST 2015

Hi Oliver,
These are both things we have felt the need for and discussed in some depth.

My understanding is that with the current complicated atomspec parsing, it is not possible (with reasonable effort) to add parentheses, but they are definitely one of the things we intend to allow in atomspecs in the next-generation Chimera.  This next-generation software is already under development.

I have also advocated for a step-by-step record of all actions (whether by menu or command) as command equivalents or some other form that allows them to be easily reproduced.  Thanks for the additional reminder that this would be a useful feature.

Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 2, 2015, at 8:13 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi all,
> Would it be possible at some point to allow the use of explicit parentheses when grouping selections on the command line? It would make it much easier/clearer when using multiple boolean operations (e.g "ligand z<5 &~ ligand &~ solvent” could be “ligand z<5 &~(ligand | solvent)”). Is there a reason why this kind of syntax is not used at the moment?
> Also, just a random thought for a future version - it would be really handy to have something like the “Macro recorder” function of ImageJ or similar programs. This records whatever the user does using the GUI (while the recorder is active) and spits out the equivalent scripting commands to a dialog, where they can be saved and reused, or turned into a script. This can be a very powerful tool for learning the command line functionality of a complex application in an interactive manner.
> Cheers,
> Oliver.

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