Hi everyone,

I'm a beginner in using MODELLER and I need help to fix my files in my modelling. I'm trying to build a homology model using two templates. I'd like to select different regions of each template to build my model. I attached the script below,

In my alignment.pir file I include the sequence of my template in the following way:

>P1;template1
structureX:protA.pdb:8:A:2822:A:::-1.00:-1.00
---------------------------------------------------------------------------
...

>P1;template2
structureX:protB.pdb:1:A:2521:A:::-1.00:-1.00
MEPHVLGAVLYWLLLPCALLAACLLRFSGLSLVYLLFLLLLPW

...

I replace the amino acid symbol for '-' when they are present in a region that I don't want to use as a template. I didn't modify my pdb files. All residues are present. 

When I run my job, MODELLER starts to create the target, but always stops at

 an error related to structure files. 

Has anyone tried the same thing that I'm trying? I'm using version 10.4

Thank you in advance.

from modeller import *
from modeller.automodel import *

log.verbose()
env = Environ()
aln = Alignment(env)
aln.append(file='alignment.pir', align_codes=('target', 'template1', 'template2'))

#class MyModel(AutoModel):
#    def select_atoms(self):
        # Select residues 1234 to 2822 from template1, mPiezo2 and 1 to 1200 from template 2 - hPIEZO1
#        return selection(self.residue_range('1234:', '2822:'),
#                         self.residue_range('1:', '1200:'))

a = AutoModel(env, alnfile='alignment.pir', knowns=('template1', 'template2'), sequence='target',
            assess_methods=(assess.DOPE, assess.GA341))

a.starting_model = 1
a.ending_model = 5
a.make()