RE: [PyMOL] Electronic density maps

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:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020
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> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Konrad Hinsen
> Sent: Tuesday, June 22, 2004 3:58 AM
> To: <pym...@li...>=20
> <pym...@li...>
> Subject: Re: [PyMOL] Electronic density maps
>=20
> On Jun 22, 2004, at 11:41, Konrad Hinsen wrote:
>=20
> > I'll see if I can get CCP4 format to work in a reasonable amount of=20
> > time...
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> Actually I went for XPlor in the end, after getting a useful hint:
>=20
> 	http://cns.csb.yale.edu/v1.1/tutorial/text.html
>=20
> Problem: the XPlor format does not specify the absolute=20
> position of the map in space. PyMOL must choose it somehow.=20
> Unfortunately, it makes the choice in such a way that my=20
> protein (in a PDB file) is outside the map.
>=20
> Is it possible to shift the map (by a numerically specified=20
> distance) after it has been loaded? I'd rather shift the=20
> single map than redoing a few dozen PDB files.
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> Konrad
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Laboratoire L=E9on Brillouin, CEA Saclay,
> 91191 Gif-sur-Yvette Cedex, France
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> Fax: +33-1 69 08 82 61
> E-Mail: hi...@ll...
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