Hi Jason, Thanks for the info and lines of script. It did the job :) .
Best Afonso On Sun, Sep 18, 2011 at 5:55 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) > > # 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 Learn about the latest advances in developing for the BlackBerry® mobile platform with sessions, labs & more. See new tools and technologies. Register for BlackBerry® DevCon today! http://p.sf.net/sfu/rim-devcon-copy1 _______________________________________________ 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
