On Sun, Sep 18, 2011 at 11:55 AM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Hi Alfonso,
>
> PyMOL knows about more spectrum types but cannot take advantage of
> them (at this point). You will need to do something different if you
> want to use a different palette. It's not hard and here's how.
>
> I'll adapt that same script using PDB 1HUG. Since you want to color
> the distance from all atoms to any given point (here chosen at the
> origin=(0,0,0)) we need to get all the atom distances from 1HUG to the
> origin. We then put those distances into the b-factor column and
> color. I posted the details of the spectrum command and this script on
> the PyMOLWiki (http://www.pymolwiki.org/index.php/Spectrum).
>
> # returns the length of the distance between atom A and atom B
>
> diff_len = lambda x,y : math.sqrt((x[0]-y[0])*(x[0]-y[0]) +
> (x[1]-y[1])*(x[1]-y[1]) + (x[2]-y[2])*(x[2]-y[2]))
>
> # fetch 1hug from the PDB
>
> fetch 1hug, async=0
>
> # show it as surface
>
> as surface
>
> # create the pseudoatom at the origin
>
> pseudoatom pOrig, pos=(0,0,0), label=origin
>
> # these are special PyMOL variables that will hold # the coordinates of
> # the atoms and the pseudoatom
>
> stored.origCoord = []
> stored.distCoord = []
>
> # copy the coordinates into those special variables
>
> iterate_state 1, pOrig, stored.origCoord.append((x,y,z))
> iterate_state 1, 1hug, stored.distCoord.append((x,y,z))
>
> # extend origCoord to be the same length as the other
>
> stored.origCoord *= len(stored.distCoord)
>
> # calculate the distances
>
> newB = map(lambda x,y: diff_len(x,y), stored.distCoord, stored.origCoord)
>
Sorry to interrupt,
PyMOL>newB = map(lambda x,y: diff_len(x,y), stored.distCoord,
stored.origCoord)
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/pymol/parser.py", line 211,
in parse
exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
File "<string>", line 1, in <module>
File "<string>", line 1, in <lambda>
NameError: global name 'diff_len' is not defined
> # put them into the b-factor of the protein
>
> alter 1hug, b=newB.pop(0)
>
> # color by rainbow_rev or any other
> # palette listed in "help spectrum"
>
> spectrum b, rainbow_rev, 1hug
>
> Cheers,
>
> -- Jason
>
>
> On Sat, Sep 17, 2011 at 1:44 PM, Afonso Duarte <afonsomdua...@gmail.com>
> wrote:
> > Dear All,
> >
> > I am using the ramp_new command to color the surface of protein A
> > according to the distance of protein B (i.e. like in the wiki example
> > ramp_new proximityRamp, pOrig, 1hug, range=[5,65], color=rainbow).
> > However I would like to color the surface of protein A in the inverse
> > rainbow color... from what understood we only can use (afmhot
> > grayscale object rainbow traditional grayable hot
> > ocean and sludge),
> >
> > Does anybody have a suggestion on how to change the colors of the ramp
> > or just to obtain a reverse rainbow ?
> >
> >
> > Best
> >
> > Afonso
> >
> >
> ------------------------------------------------------------------------------
> > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
> > http://p.sf.net/sfu/rim-devcon-copy2
> > _______________________________________________
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
>
> ------------------------------------------------------------------------------
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> http://p.sf.net/sfu/rim-devcon-copy2
> _______________________________________________
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>
--
Best Regards,
lina
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