On Fri, May 28, 2010 at 8:03 PM, Tatyana Sysoeva <span dir="ltr">&lt;<a href="mailto:tatyanasysoeva@gmail.com">tatyanasysoeva@gmail.com</a>&gt;</span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
if somebody is still not on the memorial day weekend, I have a short question off-topic for Pymol-users<br><br>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. <br>

<br>If you know some nice simple program to do nice pictures of the electron densities- share your knowledge please!<br></blockquote><div><br></div><div>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:</div>
<div><br></div><div>load 2fofc.map, 2fofc, format=xplor</div><div>isomesh m1, 2fofc, 1.0</div><div>load fofc.map, fofc, format=xplor</div><div>isomesh m2, fofc, 3.0</div><div>isomesh m3, fofc, -3.0</div><div><br></div><div>
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.</div><div><br></div><div>-Nat</div></div>