[phenixbb] offtopic: Problem with Pymol showing maps

Nathaniel Echols nechols at lbl.gov
Fri May 28 20:22:44 PDT 2010

On Fri, May 28, 2010 at 8:03 PM, Tatyana Sysoeva
<tatyanasysoeva at gmail.com>wrote:

> if somebody is still not on the memorial day weekend, I have a short
> question off-topic for Pymol-users
> I have several maps from Phenix and want to draw some pictures in Pymol. I
> am opening the files, renamed to ccp4 or map, or not, and all I am getting
> is just a box, which is not even a unit cell boundary.
> If you know some nice simple program to do nice pictures of the electron
> densities- share your knowledge please!

My guess is that the maps are covering only a box around the molecule (with
some padding); this is probably what you want anyway.  You need a second
command to draw the mesh:

load 2fofc.map, 2fofc, format=xplor
isomesh m1, 2fofc, 1.0
load fofc.map, fofc, format=xplor
isomesh m2, fofc, 3.0
isomesh m3, fofc, -3.0

In recent versions you can also click one of the menus next to the map
object on the right, and it will have preset options for all this.

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