[modeller_usage] modelling from 2 templates, one for major part of sequence, 1 for insertion region

[Irene Newhouse <>]

I'm trying to model a protein that looks like a member of CIS_IPPS with reasonable homlogy for a major portion of the sequence, but with a significant insertion region that has weak homology to a portion of a different protein. I tried to build with the .py & .ali files listed below, with the result that the CIS_IPPS regions of the protein were built just fine, but the insertion region was nothing but a random coil. When I extracted the insertion region & modeled it based on the extracted portion of the other protein, I was able to model something reasonable. I could use a GUI to meld the two models together, but I'd rather have recommendations as to how to get modeller to do the build for me - I think it'd be a lot better starting structure than the result of a hand-meld. Thanks in advance!

Irene Newhouse

.py file:
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

log.verbose()    # request verbose output
# Override the 'special_restraints' and 'user_after_single_model' methods:
class MyModel(automodel):
    def special_restraints(self, aln):
        # Constrain the A and B chains to be identical (but only restrain
        # the C-alpha atoms, to reduce the number of interatomic distances
        # that need to be calculated):
        s1 = selection(self.chains['A']).only_atom_types('CA')
        s2 = selection(self.chains['B']).only_atom_types('CA')
        self.restraints.symmetry.append(symmetry(s1, s2, 1.0))
    def user_after_single_model(self):
        # Report on symmetry violations greater than 1A after building
        # each model:
        self.restraints.symmetry.report(1.0) 

env = environ()  # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = ['.', '/home/newhoir/rubber/']

#read HETATMS in template
env.io.hetatm = True

# Be sure to use 'MyModel' rather than 'automodel' here!
a = MyModel(env,
            alnfile  = 'rub4b.ali' ,     # alignment filename
            knowns   = ('2x06', '2erx'),   # codes of the templates
            sequence = '1cp4',              # code of the target
            assess_methods=assess.GA341)     # request model assessment
a.starting_model= 1                 # index of the first model
a.ending_model  = 20               # index of the last model
                                    # (determines how many models to calculate)
a.library_schedule = autosched.slow # thorough VTFM opt
a.max_var_iterations = 300
a.md_level = refine.very_slow
a.make()                            # do the actual homology modeling

The .ali file:
>P1;2x06
structureX:2x06:12:A:+474:B:PDB::0.00:0.00
-------------------------KLPAHG--CRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKS---LHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVR--------------------------------------------------------------QLAEKVQQGNLQPDQIDEEMLN-----------------------------------------------QHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE----------.../-------------------------KLPAHG--CRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKS---LHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVR--------------------------------------------------------------QLAEKVQQGNLQPDQIDEEMLN-----------------------------------------------QHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE----------...*
>P1;2erx
structureX:2erx:16:A:+66:B:PDB::0.00:0.00
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGVGKSSLVLRFVKGTFRESYIPTVEDTYRQVI------------------------------------------------------------------------------------------------------/---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGVGKSSLVLRFVKGTFRESYIPTVEDTYRQVI------------------------------------------------------------------------------------------------------*
>P1;1cp4
sequence:1cp4:1:A:+758:B:::0.00:0.00
MGKHSSSRVSELFGNLGSFIRACIFRVLSMGPIPNHFAFIMDGNRRYAKKENMKKGAGHRAGFLALISILKYCYELGVKYVTIYAFSIDNFKRNPDEVKDLMDLMLEKIEELLRDESIVNQYGIRVYFIGNLKLLSEPVRIAAEKVMRATAKNTNCTLLICIAYTSRDEIVHAVQGSCKNKREDILPLSFCKANNGDIEEVEDDKKVHGVSPFVFSESQKDEAGESQATIASVTCSCLARGVEGGGNKNSMVVRAVRGSYEDKW-----DNYQAVMENRTGSGVTPSEENKNMQGECSIVKLVDIEKQMYMAVAPEPDILIRSSGESRLSNFLLWQSSECLLYSPDALWPEIGLWHLVWAVLNFQRNHSYLERKKHQL.../MGKHSSSRVSELFGNLGSFIRACIFRVLSMGPIPNHFAFIMDGNRRYAKKENMKKGAGHRAGFLALISILKYCYELGVKYVTIYAFSIDNFKRNPDEVKDLMDLMLEKIEELLRDESIVNQYGIRVYFIGNLKLLSEPVRIAAEKVMRATAKNTNCTLLICIAYTSRDEIVHAVQGSCKNKREDILPLSFCKANNGDIEEVEDDKKVHGVSPFVFSESQKDEAGESQATIASVTCSCLARGVEGGGNKNSMVVRAVRGSYEDKW-----DNYQAVMENRTGSGVTPSEENKNMQGECSIVKLVDIEKQMYMAVAPEPDILIRSSGESRLSNFLLWQSSECLLYSPDALWPEIGLWHLVWAVLNFQRNHSYLERKKHQL...*