Thanks for the suggestion! It worked great.
-Karen Fleming
On Feb 10, 2009, at 11:24 AM, Paul Emsley wrote:
Karen Fleming wrote:
I am trying to make a homework problem for undergrads and have
three molecules:
0. mymap.mtz 2FOFCWT PH2FOFCWT
1. mymap.mtz FOFCWT PHFOFCWT
2. mymolecule.pdb
The pdb file originally had a protein and a ligand. I manually
deleted the
ligand in the pdb file, so now the density does not have
coordinates for it.
I would like to create a mask of this density so that I can save
it separately.
Surely this must be simple, but I can't figure it out:
:(
I am running coot on Mac OS X 10.4.11. I opened the script window
using
Calculate-->Scripting-->Scheme and typed mask-map-by-molecule 0 2
0 only to get:
coot> mask-map-by-molecule 0 2 0
#<primitive-procedure mask-map-by-molecule>
coot> 0
coot> 2
coot> 0
coot> Don't type here. Type in the white entry bar.
This is the format for scheme scripting
(but don't forget the parentheses :) (or do I mean :))
I tried it using the "pymol" format:
mask-map-by-molecule(0,2,0)
#<primitive-procedure mask-map-by-molecule>
coot> Backtrace:
In current input:
5: 0* (0,2,0)
<unnamed port>:5:21: In expression (0,2,0):
<unnamed port>:5:21: Unbound variable: 0,2,0
ABORT: (unbound-variable)
mask_map_by_molecule(0,2,0)
would be fine if you'd have typed it in the python window.
Does that help?
Paul.
