Hi everyone,
I just upgraded to the latest JSmol and noticed a strange bug with the
assign atom function. When I have a particular selection set, and then I
run "assign atom", JSmol selects the entire molecule instead of the
selection I had before. Since I rely on selectionhalos to let a user know
about a particular substructure (in my case a protonatable protein side
chain), this leads to a bad situation where the entire molecule, instead of
just the sidechain, is now selected. I know I can just run "select resno=X"
after my script, but it is strange that this occurs in the first place.
Perform the following with protein 1u19 from PDB (I tested on
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm):
select resno=5;display within(5.0,selected);cpk 30%;wireframe 55;ribbons
off;cartoons off; color jmol;center selected; zoom 0;selectionhalos on
assign atom (:A.OE2 and resno=5) "Pl"
This causes a crash in Chrome 48.0.2564.116m, and the entire molecule to be
selected in Firefox 44.0.2.
Is there an alternate way of assigning protonation states? What is going on
here?
Thanks,
Vinushka Schalk
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