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@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 #