[Chimera-users] electron density map

Oliver Clarke olibclarke at gmail.com
Thu Apr 28 06:37:03 PDT 2016

Dear Liuqing,

Step size refers to whether every point in the map is displayed (step 1), or every second point (step 2), or every fourth point (step 4) and so on - basically, the coarseness of the grid. Loading a map at a larger step size will have less detail, but will be faster to load and manipulate. See here (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#sampling) for details.

The level in Chimera is the same as in coot in absolute terms (e-/Å^3) - it is just that in Coot, by default, maps are adjusted in steps of r.m.s. (often called “sigma”), whereas the default behaviour in Chimera is to deal directly with absolute electron density levels. You can mimic the Coot behaviour, however, by adjusting the volume level on the command line with the option sdlevel, for example “volume #1 sdlevel 1” will set the volume with id #1 to 2xr.m.s. See here (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#level) for details. For convenience (really due to my forgetfulness), I use an alias to do this, as follows:

"alias ^map_sig volume $1 sdlevel $2"

so then one can use the command “map_sig #1 5” to adjust map #1 to 5xr.m.s., which should match the corresponding level in coot.

If you want to mimic how maps look in coot, adjusting some of the mesh options is handy, as follows:

"alias ^cootmode volume $1 capfaces false style mesh meshlighting false squaremesh false color "#08882eefa222" step 1; sop cap off; set depthCue; set dcStart 0.2; set dcEnd 1; background solid white; cofron”

Where “cofron" is an alias that mimics the centering and navigation behaviour of coot:

"alias ^cofron set showcofr; cofr view; clip on”


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