[Chimera-users] Custom presets

Elaine Meng meng at cgl.ucsf.edu
Tue May 20 08:51:35 PDT 2014


Hi Oliver,
Just a couple of minor notes on your script:

(1) you don't need the # in  the disp, ribbon, represent, modelcolor, color commands; for many commands in which the atomspec is the last part, blank atomspec (nothing) means "all applicable items" (likewise, you wouldn't need the @ in window unless you want it to use only atoms)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

(2) if # works for the volume command, that's fine, but it can also take the word "all"
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html>

Best,
Elaine

On May 19, 2014, at 9:10 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Using # doesn’t seem to work with vop if there are any non-volume models, as it complains that they are not surfaces. Using the selection ~@ (everything that isn’t an atom) seems to work fine though.
> 
> In case it is of use to anyone else, here are the presets I came up with for X-ray maps. Seems to work okay as a starting point to then tweak by adjusting clipping, using vop zone on an atom selection, etc. Would like to normalize to RMS automatically but that will require a little more thinking.
> 
> window @
> set dcstart 0.4
> set dcend 1.0
> sop cap off
> vop zone ~@ @ 5
> volume # style mesh
> volume # squaremesh false
> volume # linethickness 1.5
> volume # meshlighting false
> volume # capfaces false
> background solid black
> scolor # color blue
> disp #
> ~ribbon #
> represent stick #
> modelcolor gold #
> color byhet #
> 



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