[Chimera-users] explicit parentheses in atom selections

Oliver Clarke olibclarke at gmail.com
Mon Mar 2 09:03:34 PST 2015

Many thanks for the quick reply Elaine, and I look forward to seeing the next-gen Chimera, I’m sure it will be great!

In terms of command-line features that would be useful for the next-gen chimera, maybe you could have a look at IPython for inspiration? A more complex shell-like interface with tab-completion and an easily searchable history would be wonderful…

> On Mar 2, 2015, at 11:48 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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.
> Best,
> 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 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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