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. 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.
