[Chimera-users] Custom presets

Oliver Clarke olibclarke at gmail.com
Mon May 19 16:18:52 PDT 2014

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?

On May 19, 2014, at 1:00 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Oliver,
> I didn't see another post, so no worries about that!
> You can't save the current display settings directly as a custom preset.  You would need to create a plain text file of Chimera commands or Python code for the settings, then name it appropriately and tell Chimera where the file is located (menu Presets… Add Custom Presets).
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets>
> Some of the main Chimera commands related to display are:
> color - coloring atoms, bonds, ribbons, molecular surfaces
> display - which atoms/bonds are shown
> represent - atom/bond display style
> ribbon - ribbon stuff
> surface - molecular surface stuff
> setattr - attributes not covered by the above (for example: setattr m stickScale 0.5)
> set - many global settings like background color, depth-cueing, shadows, outlines
> volume - density display (see meshLighting, capFaces, squareMesh options)
> See command documentation and also the image tips:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
> A similar feature for definining macros that can be expressed as a series of commands is the alias mechanism.  With the "alias" command you can define longer sets of commands as a shorter command, even including command arguments.  The shorter command can be entered in the command line, and some of the aliases (those defined with "^" and without arguments) will even appear in a new Aliases menu. 
> For details and examples see:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
> You can actually get quite fancy with both of these mechanisms.  The main barrier is figuring out the appropriate commands or code.  You can test either type of file by simply opening it in Chimera, and of course you can test individual commands by entering them in the command line.
> As for your normalization procedure, sounds like Python would be required to automatically insert the SD, min, and max into the other commands. Python is beyond my skill set, so others may need to respond to that part of your question.
> 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 7:18 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
>> Hi all,
>> I posted this last week, but it didn’t appear in the archives, so I guess it didn’t go through - if that is not the case, my apologies for the double post.
>> I notice in the presets menu that there is the option to add custom presets, but I couldn’t find much documentation on this feature.
>> Is it possible to save the current display options as a preset, similar to saving individual preference combinations but as a preset that can be quickly loaded?
>> For example, displaying X-ray maps in a way that looks similar to how they are represented in Coot is a little complicated - I usually turn off “Mesh lighting”, “Cap high values at box faces”, and “Square mesh”, turn off ribbons, display all atoms and set the stick scale to 0.5, change the background to black, and alter the depth cueing - it would be very handy indeed to be able to apply all these settings at once.
>> Also with regards to X-ray maps, I usually normalize (using vop scale #map, factor 1/SD) both the 2fo-fc and fo-fc, and then split the fo-fc into separate +ve and -ve maps, using vop threshold #map minimum 0 and vop threshold #map maximum 0. Would it be possible to assign these steps to macros or commands, and if so how would I go about doing that?
>> Many thanks for your help,
>> Oliver.

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