Hello Kimberly, Please try using [blue, white, red] in ramp_new:
cmd.ramp_new("ramp_obj", "ca_obj", range=[minval, maxval], color="[blue,white,red]") ramp_new recognizes only a limited set of pre-defined palettes (see https://pymolwiki.org/index.php/Ramp_New ) and they need to be specified without the brackets, e.g. cmd.ramp_new("ramp_obj", "ca_obj", range=[minval, maxval], color="rainbow") Thanks, Piotr On Tue, Feb 7, 2017 at 11:31 PM, Kimberly Jesseman <kmjesse...@plymouth.edu> wrote: > Hello, > > > I have successfully colored the surface of a PDB by b factors I replaced by > modifying the loadBfacts script. However, my color bar is only showing up > as white instead of accurately showing the blue-white-red color scheme of my > PDB (I've attached a picture). This is my script: > > > from pymol import cmd, stored, math > > > def loadBfacts (mol,startaa=1,source="newBfactors.txt"): > > """ > > Replaces B-factors with a list of values contained in a plain txt file > > > usage: loadBfacts mol, [startaa, [source, [visual]]] > > > > mol = any object selection (within one single object though) > > startaa = number of first amino acid in 'new B-factors' file (default=1) > > source = name of the file containing new B-factor values > (default=newBfactors.txt) > > > > example: loadBfacts 1LVM and chain A > > """ > > obj=cmd.get_object_list(mol)[0] > > cmd.alter(mol,"b=-1.0") > > inFile = open(source, 'r') > > counter=int(startaa) > > bfacts=[] > > > for line in inFile.readlines(): > > bfact=float(line) > > bfacts.append(bfact) > > cmd.alter("%s and resi %s"%(mol,counter), "b=%s"%bfact) > > counter=counter+1 > > > minval = min(bfacts) > > maxval = max(bfacts) > > cmd.show_as("surface",mol) > > cmd.spectrum("b","blue_white_red", "%s and n. CA"%mol, minimum=minval, > maximum=maxval) > > cmd.create("ca_obj", mol + " and n. ca") > > cmd.ramp_new("ramp_obj", "ca_obj", range=[minval, maxval], > color="[blue_white_red]") > > cmd.set("surface_color", "ramp_obj", mol) > > > cmd.extend("loadBfacts", loadBfacts); > > > Any insight into why this is occurring and how to fix it would be greatly > appreciated. > > Thank you! > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ 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