Re: [PyMOL] APBS

[Martin M. <mg...@mr...>]

Hi Brian,

Try this, the info is from the mailing list archive (http:// 
sourceforge.net/mailarchive/forum.php?forum_id=60)it just takes a bit  
of finding....


load x.pdb

load whatever.dx, e_pot

ramp_new e_lvl, e_pot, [-15, 0, 15], [ [1,0,0], [1,1,1] , [0,0,1] ] #  
this sets the scale and colours for the e_potential scale.

show surface, x.pdb

set surface_color, e_lvl, x.pdb



# load whatever.dx, e_pot - this loads the .dx map and calls it e_pot  
(this might not load via command line. If not, use the open command  
from the file menu then rename as desired)
# ramp_new e_lvl sets the scale and colors
# [-15, 0, 15] sets the potential scale
# [1,0,0] is red, [1,1,1] is white, [0,0,1] is blue so -15 is red, 0  
is white and +15 is blue




hope it helps


MGM



On 19 Nov 2005, at 19:53, Brian J Goodfellow wrote:

> Dear Users,
>
> I was wondering does anyone know how to get nice APBS generated  
> electrostatic surfaces in MacPyMOL. I know the APBS plugin can't/ 
> won't work in MacPyMOL so I guess it's a question of what do I do  
> with the output from APBS (I assume it's the dx file) to get a  
> surface in MacPyMOL.
>
> Till now I've been generating the surfaces in PyMOLX11Hybrid with  
> the plugin and saving a pse file and then reading it into MacPyMOL,  
> which is not the end of the world I guess, but it's just a bit of a  
> pain......
>
> Cheers,
>
> Brian
>



Martin Montgomery
Director's Group
MRC Dunn Human Nutrition Unit
Hills Road
Cambridge
CB2 2XY