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
<[email protected]> 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!
>
>
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