Hi all,
It's possible that I've run into a bug/undocumented feature, but I'd
like to see if anyone has a solution to the following problem.
I'm working on a movie script that will (in part) make two separate
surfaces for each subunit in a dimer (excluding a drug bound between
the subunits), then split the monomers apart and zoom into a drug
binding site. However, I'm running into some problems when I try to
create the separate surfaces.
In plain english, what the script does is create two objects, one
containing one subunit (B), and the other containing the other subunit
AND the drug (A) (when I split the monomers apart I want the drug to
follow one monomer). I then calculate the surface for subunit B, flag
everything that's not subunit A as ignore, then calculate the surface
for subunit A.
If I input each line separately, the script works perfectly and I get
two separate surfaces around each subunit and no surface around the
drug. But if I run the script from the PyMOL command line or copy/paste
the whole script at once into the command line, only subunit A shows a
surface. The drug (correctly) does not have a surface, but (from the
output in the terminal) it looks like PyMOL isn't even calculating a
surface for subunit B.
Any ideas would be greatly appreciated.
Below are the relevant lines of the script:
## make all of the objects we'll need
cmd.create("A+amp+drug","a// or l/1/ or d//")
cmd.create("B+amp","b// or l/2/")
cmd.select("drug","d//")
cmd.select("A+amp","d// or l/1/")
cmd.select("none")
cmd.delete("lc03")
cmd.orient()
## color it up
cmd.color("orange","A+amp+drug and A+amp")
cmd.color("wheat","B+amp")
## let's show separate surfaces for each subunit
cmd.show("surface","B+amp")
cmd.flag("ignore","not A+amp","set")
cmd.show("surface")
Many thanks,
Jacob
