[Chimera-users] Custom presets

Oliver Clarke olibclarke at gmail.com
Mon May 19 17:13:27 PDT 2014

Thanks Tom and Elaine, # was what I was looking for - I didn’t realize you could use that to specify all models. I will try that and see how I go.

On May 19, 2014, at 8:06 PM, Tom Goddard <goddard at sonic.net> wrote:

> For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number.
> 	Tom
> On May 19, 2014, at 4:45 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hi Oliver,
>> You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0).  Choosing the preset is the same as executing all the commands in the file.  For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red).  Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models.
>> If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases.  See the "alias" documentation for how to specify arguments to your macro:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
>> One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms.  Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification.  See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword.
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
>> You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open.
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
>> 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 May 19, 2014, at 4:18 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
>>> Hi Elaine,
>>> Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? 
>>> Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that?
>>> Best,
>>> Oliver.
>>> On May 19, 2014, at 1:00 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
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