Re: [PyMOL] Question about electron density map with mtz file

[Robert C. <rob...@qu...>]

Hi Adiphol

* adi di <adi...@ya...> [2007-05-11 10:26] wrote:
> Dear all,
> 
> I am trying to put on the electron density. I only
> have .mtz file but I have a look at the manual and the
> program need XPLOR file. How can I get the XPLOR file
> or do I need to convert the mtz file to this - if so
> how can I do that? Thank you very much

Actually PyMOL can read ccp4 format maps, but they have to be maps, not
the mtz reflection file with the columns h, k, l, FWT, PHWT etc. as
output by refmac and other programs.  If you ask refmac to output a CCP4
format map, then PyMOL can read it:

load filename.map, map_obj, format=ccp4

will load the map and create an object called map_obj.  The latter then
needs to be contoured by PyMOL.  For example:

  isomesh lev1, map_obj, selection=molecule & c. a  & resi 100, level=1, buffer=8.

would create an object called lev1 with a contour level of 1 in a box of
8Angstroms around residue 100 of chain a of "molecule".

Hope that helps,

Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc