Hi, I tried using 'or'. I didn't get any errors, but now that I'm checking the
outputs, I found that I got the area for just the ligand and not the complex,
when I use 'get_area' on the complex. I noticed I get the area for whichever
(ligand/target) is before the "or" operator, not the one after and definitely
not for the complex. Here's the code I've been using:
## r=target(name read as user input)
## s=ligand(name read as user input)
e=r+".pdb"
f=s+".pdb"
cmd.load(e)
cmd.load(f)
cmd.h_add
cmd.flag(25, NONE)
cmd.set("dot_solvent", 1)
cmd.set("dot_density", 3)
ligand_area=cmd.get_area(s)
target_area=cmd.get_area(r)
cmd.create("complex", s or r)
complex_area=cmd.get_area("complex")
contact_area=((ligand_area+target_area)-complex_area)/2
print ligand_area
print target_area
print complex_area
print contact_area
Thanks in advance.
Ritu
On 02/13/12, Thomas Holder wrote:
> Hi Ritu,
>
> put "ligand" and "target" in one string as an atom selection with a
> logical "or".
>
> cmd.load("ligand.pdb")
> cmd.load("target.pdb")
> cmd.create("complex", "ligand or target")
>
> Cheers,
> Thomas
>
> Rituparna Sengupta wrote, On 02/13/12 19:28:
> >Hi,
> >
> >I've just started using PyMol, so this may come across as a stupid
> >question. I'm using Python to make a plugin for a surface area
> >calculation. What is the api version for the command:
> >
> >create complex, ligand target
> >
> >?(ligand and target are pdb files) I tried using,
> >
> >cmd.create(complex, ligand, target)
> >
> >but found errors. Apparently I'm supposed to put an integer after the
> >first two entries in the bracket(according to the 'create' command
> >api version instructions in the pymol wiki commands section). I tried
> >loading the molecules separately into 'complex', but the value of the
> >complex area is different from when loaded together(found this out by
> >typing directly into pymol). I'll be glad if someone could help.
> >
> >Thanks, Ritu
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
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