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: [email protected]
