Re: [PyMOL] Extra electron denity map is not visible in pymol

[Eric L. <larsonet@u.washington.edu>]

Hi Peter,

Are you trying to view in Pymol a map that you have saved from coot?  The coot map only covers the AU so if the part of the map that you are trying to visualize in pymol is outside of the AU, you will not see it.  The solution is to use fft in ccp4 to create your map and be sure to make it cover your model (this is an option from a pull-down menu in the fft ccp4i gui).  You should then be able to use this map in pymol to see the features you want.

Hope that solves your problem,
Eric
__________________________
Eric Larson, PhD
MSGPP Consortium
Department of Biochemistry
Box 357742
University of Washington
Seattle, WA 98195

> Message: 5
> Date: Tue, 16 Mar 2010 23:08:05 +0530
> From: peter hudson <pet...@gm...>
> Subject: [PyMOL] Extra electron denity map is not visible in pymol
> To: pym...@li...
> Message-ID:
> 	<c70...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello everybody
>
> I have two different isoforms of a crystals of different of 3.0A (SAD
> Dataset) and 2.5A resolution. In one crystal form a dimer is present is ASU,
> where as in another crystal form it is present as  a tetramer. I want to
> make a image which should show the extra elctron density which is present in
> tetrameric form. This extra density which is visible in coot as well as in O
> but not in pymol  with the same map file. Although i tried unset the
> normalisation of the ccp4 map, thge map remain as such without extra density
> of the another molecule. I would appreciate the suggestions.
>
> Thanks in advance
>
> peter