[buster-discuss] buster maps in pymol

Donald Damian Raymond donal at umich.edu
Tue Sep 27 22:22:16 CEST 2011


I am having the same issue opening an MTZ generated by buster in the  
latest version of PyMOL.

In refmac where is an option to generate a map around the atoms in the  
PDB that will ensure that the map is only generated around atoms in  
the pdb.

It appears that the MTZ generated by buster only draws the map in the  
unit cell when loaded in PyMOL. However, in many cases some of the  
modeled atoms are not in the unit cell. See attached image.

It may be both a buster and PyMOL issue.

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On Sep 27, 2011, at 3:16 PM, Clemens Vonrhein wrote:

> Hi,
> On Tue, Sep 27, 2011 at 12:04:31PM -0400, Elias Fernandez wrote:
>> Hello, I should have elaborated. I'm trying to display buster Fo-Fc  
>> and
>> 2Fo-Fc maps from Buster in Pymol. However, when I use the Buster
>> instructions, the map seem sot be in a different frame of reference  
>> than the
>> coordinates. Any ideas? Thanks! Elias
> BUSTER 2Fo-Fc maps (2FOFCWT/PH2FOFCWT columns) and Fo-Fc maps
> (FOFCWT/PHFOFCWT) are not different from any other
> amplitude/phase-based map in MTZ format. If you can open other maps
> from program XYZ, then using the 'refine.mtz' from BUSTER will be
> identical - apart from column names maybe.
> So your problem with a difference/shift between coordinates and the
> maps is unlikely to be related or specific to BUSTER: maybe the pymol
> mailing list can help?
> As an example of using BUSTER maps (albeit in Coot):
>  % coot --pdb refine.pdb --auto refine.mtz
> and everything will work as expected.
> Clemens
> -- 
> ***************************************************************
> * Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
> *
> *  Global Phasing Ltd.
> *  Sheraton House, Castle Park
> *  Cambridge CB3 0AX, UK
> *--------------------------------------------------------------
> * BUSTER Development Group      (http://www.globalphasing.com)
> ***************************************************************
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