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Re: [modeller_usage] allhydrogen model and nselat error

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@ucsf.edu> 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@ucsf.edu             http://www.salilab.org/modeller/
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