Starr Hazard wrote: > I am experimenting with leaving crystal waters in my template structures. > > I am also trying the python scripting for the first time. > > I have been trying to get MODELLER8v1 to accept a single template. > The template has hydrogens as do the waters. This works out to > 6324 atoms. > > The rsr file has lots of entries for atom 6324. This suggests that > counting atoms is not a problem. > > The execution stops with an csrng and a nselat error indicating > that the atom index is out of bounds and out of range. The atom numbers > are for 6320 an 6319. 6319 is an oxygen; 6320 one of its hydrogens.
I cannot reproduce your problem unless you send me your input files. See http://salilab.org/modeller/manual/node11.html
Your script looks OK, except that you should not put quotes round assess.DOPE or assess.GA341.
Ben Webb, Modeller Caretaker