Thanks. As it turned out, in my alignment,the template had the listed the proper number of aa but the program got confused some where about this. Say I had 1:B:159:B with 279 waters. If I changed the above to 1:B:444:B (ie added the number of waters to the number of aa) then the errors went away. This is implicit in the FAQ 9 but I had not taken notice of the numbers, just the w's.
Thanks for the tip about quotes, that works now too.
Starr
--On Wednesday, July 13, 2005 2:16 PM -0700 Modeller Caretaker modeller-care@salilab.org wrote:
> 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 > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >