If you are not familiar with the scripting, why not try:
Extensions->Maps->Mask Map by Atom Selection
With respect to scripting (your syntax is off):
see e.g.:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Python_to_Scheme_and_return
Hope this helps,
B
> 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
> usingCalculate-->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.
>
> I tried it by protein:
>
> mask-map-by-protein 0 2 0
> ERROR: Unbound variable: mask-map-by-protein
> ABORT: (unbound-variable)
> coot> 0
> coot> 2
> coot> 0
>
> 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)
>
> Can anyone suggest a different syntax to get this to work?? Thanks.
>
***************************************************
Dr. Bernhard Lohkamp
Assistant Professor
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487673
fax: (+46) 08-327626
email: [log in to unmask]
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