I am just starting to use Jmol and I would really appreciate some help...
I have a protein file, and I have a ligand file. Task 1 is to select
only those protein atoms within 6Ang of the ligand. Task 2 is to
display only these selected atoms. Task 3 is to draw the isosurface of
the selected atoms.
I just cannot get as far as Task 2. Here's what I've done:
load file:///D:/NegativeData/RUNS/dock_inactives_paper/1w2g/protein.mol2
load APPEND file:///D:/NegativeData/data/new_set_ccdc/1w2g/ligand.mol
select within(6.0, true, */2)
The last line selects 291 atoms; since there are only 31 atoms in the
ligand and there are 5840 atoms in the protein it looks like Task 1
has been accomplished.
At this point the applet just shows the ligand. If I try "display" it
just says "0 atoms hidden" and doesn't change anything. Any ideas?
Noel
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