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.


(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.)

Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: 
> [] On Behalf Of 
> EPF (Esben Peter Friis)
> Sent: Tuesday, May 11, 2004 12:16 PM
> To:
> 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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