[modeller_usage] allhydrogen model and nselat error

[Starr Hazard <>]

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