Re: [PyMOL] rotating map

[Warren D. <wa...@de...>]

Jan,

Perform the structure alignment after loading the structure and map:

load 1zziA_pbeq.pdb
load 1zziA_pbeq.dx, 1zziA_map 

# add

load target.pdb

align 1zziA_pbeq////CA, target////CA

matrix_copy 1zziA_pbeq, 1zziA_map

# Then continue with the rest of your script.

Cheers,
Warren

> -----Original Message-----
> From: Jan Kosinski [mailto:ko...@ge...] 
> Sent: Tuesday, April 28, 2009 8:03 AM
> To: Carlos Huerta
> Cc: pym...@li...
> Subject: Re: [PyMOL] rotating map
> 
> I cannot do that, because the CHARMM-GUI server that I use 
> for calculating the electrostatic potential changes the 
> orientation of the input structures (I reported that to the authors).
> 
> Cheers,
> Janek
> 
> Carlos Huerta wrote:
> > Janek,
> >
> > You need to align your structure with the reference, then 
> re-calculate the electrostatic potentials.
> >
> > Sincerely,
> >
> > Carlos
> >
> >   
> >>>> Jan Kosinski <ko...@ge...> 04/28/09 9:04 AM >>>
> >>>>         
> > I am visualizing in PyMol electrostatic potential generated by PBEQ 
> > Solver from CHARMM-GUI at 
> > http://www.charmm-gui.org/?doc=input/pbeqsolver
> >
> > The maps loads and colors nicely with the following 
> commands suggested 
> > by the PBEQ Solver server:
> > load 1zziA_pbeq.pdb
> > load 1zziA_pbeq.dx, 1zziA_map
> > show surface, 1zziA_pbeq
> > ramp_new 1zziA_elvl, 1zziA_map,[-2,0,2] set surface_color, 
> 1zziA_elvl, 
> > 1zziA_pbeq set surface_solvent, 1, 1zziA_pbeq
> >
> > Now I want to fit my structure to some reference one using super or 
> > align commands. As expected, the map no longer works, I cannot 
> > re-generate the original coloring after fitting. I suppose 
> that I need 
> > to change the orientation of the map accordingly to the rotation of 
> > the structure. But... how to do that? Is it at all possible?
> >
> > Cheers,
> > Janek
> >
> > 
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