Hi Warren,
Another (temporary) solution, which shouldn't be too hard to implement,
would be the ability of 'glueing' the colors to the object. That is,
bind the color for each atom in the object, originating from the map, to
that atom.
Brings me to a question. Is it currently possible to request the color a
specific atom has? That would also make it possible to implement this
using python.
Cheers,
Tsjerk
Warren DeLano wrote:
Esben,
You've identified the only good workaround at present. This is a
high-priority need that should be addressed in the next couple of months as
the internal matrix code in overhauled. My apologies for the inconvenience.
Cheers,
Warren
(PS. It is possible to transform the map, but you would need the full
matrix in order to do it, and PyMOL doesn't currently output the matrix when
it performs an alignment.)
--
mailto:war...@delanoscientific.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
EPF (Esben Peter Friis)
Sent: Tuesday, May 11, 2004 12:16 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Rotation of maps when aligning
Hi PyMOLers
I have a bunch of structures, for which I have calculated
electrostatic potential maps (using Gromacs and MEAD). I can
easily load the structures and corresponding maps into PyMOL
and display a color coded surface. But when I try to align
the structures, only the atomic coordinates are transformed -
the electrostatic maps remain in their original orientations.
As PyMOL update the surfaces after the alignment, the
resulting surface colors are completely wrong. Doing things
in another order doesn't help.
As far as I can see from a posting from March 3rd (by John
Eksterowicz), the problem is exactly the same for a density map.
In my case, the workaround is to align all the structures
before I do the electrostatic calculation - but it would be
better if the maps could be assigned to the coordinate system
of a structure. In this way, the maps would still be vaild
after a 3D-alignment. Is there a way to do this?
Best regards
Esben
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