Re: [modeller_usage] allhydrogen model and nselat error

[Starr Hazard <>]

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 
<> 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
> --
>              http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage