Folks,

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.

"csrrng__299E> Atom index is out of bounds: 6320 6319 nselat__596E> Atom index is out of range (iatm,natm): 6320 6319"

Both 6319 and 6320 have lots of entries in the rsr file. 6320 appears to have many more entries than 6319.

Here is the primative python script I am exploring.

# Very fast homology modelling by the automodel class

from modeller.automodel import * # Load the automodel class

log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' env.io.water= True

a = allhmodel(env, alnfile='wwat.pir', # alignment filename knowns= ('PDB'), # codes of the templates sequence='G1', # code of the target # assess_methods=('assess.DOPE', 'assess.GA341') # request DOPE and GA341 model assessment ) a.very_fast() # prepare for extremely fast optimization

a.starting_model = 1 a.ending_model = 5 a.final_malign3d = True

a.make() # make the homology model

What can do to troubleshoot this?

Starr