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) # 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 ------------------------------------------------------------------------------ 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
