On Fri, May 28, 2010 at 8:03 PM, Tatyana Sysoeva 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. -Nat

Hi Tanya,

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,

I'm slightly puzzled about this... Are you trying to open X-plor formatted maps? By default phenix.refine writes out only MTZ with map coefficients. Basically, my question is: how you obtained the maps that you are trying to see in PyMol?

If you know some nice simple program to do nice pictures of the electron densities- share your knowledge please!

I always use PyMol for this - it is simple, and you can find all basic commands and temples on the web. Pavel.