Konrad,
Using crystallographic formats like XPLOR for generic volume
visualization is tricky because ultimately the map must be aligned on a grid
which passes through the origin. In other words, the grid spacing must
include the origin even if the map itself does not. In order to shift the
map away from the origin, you need to move the interval away from the
origin.
For example, to get a map covering the interval 25 to 75 along an axis in
XPLOR format, you would need to provide the information as follows:
There unit cell axis is 50 Angstroms.
There are 50 divisions per unit cell.
The range for this axis is 25 to 75.
etc.
Cheers,
Warren
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Konrad Hinsen
> Sent: Tuesday, June 22, 2004 3:58 AM
> To: <pymol-users@lists.sourceforge.net>
> <pymol-users@lists.sourceforge.net>
> Subject: Re: [PyMOL] Electronic density maps
>
> On Jun 22, 2004, at 11:41, Konrad Hinsen wrote:
>
> > I'll see if I can get CCP4 format to work in a reasonable amount of
> > time...
>
> Actually I went for XPlor in the end, after getting a useful hint:
>
> http://cns.csb.yale.edu/v1.1/tutorial/text.html
>
> Problem: the XPlor format does not specify the absolute
> position of the map in space. PyMOL must choose it somehow.
> Unfortunately, it makes the choice in such a way that my
> protein (in a PDB file) is outside the map.
>
> Is it possible to shift the map (by a numerically specified
> distance) after it has been loaded? I'd rather shift the
> single map than redoing a few dozen PDB files.
>
> Konrad
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Laboratoire Léon Brillouin, CEA Saclay,
> 91191 Gif-sur-Yvette Cedex, France
> Tel.: +33-1 69 08 79 25
> Fax: +33-1 69 08 82 61
> E-Mail: hin...@llb.saclay.cea.fr
> ---------------------------------------------------------------------
>
>
>
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