[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[modeller_usage] one question about merging two proteins into one



Dear modeller administrator:

I tried to merge two protein dimers into one dimer, with only 7 residues overlapped in each monomer.  The aligned.ali file is like following:

>P1;pl5t
structureX:pl5t:   1 : :+78  : :::-1.00:-1.00
GESPGAFPVAAQVGLGVGTSLLALGVIIIVLMYRRKSKQ---------------------------GESPGAFPVAAQVGLGVGTSLLALGVIIIVLMYRRKSKQ---------------------------*

>P1;pbjm
structureX:pbjm:   1 : :+68  : :::-1.00:-1.00
--------------------------------YRRKSKQALRDYKKVQIQLENLESSVRDRCKKEF--------------------------------YRRKSKQALRDYKKVQIQLENLESSVRDRCKKEF*

>P1;plxd
sequence:plxd
GESPGAFPVAAQVGLGVGTSLLALGVIIIVLMYRRKSKQALRDYKKVQIQLENLESSVRDRCKKEFGESPGAFPVAAQVGLGVGTSLLALGVIIIVLMYRRKSKQALRDYKKVQIQLENLESSVRDRCKKEF*

I also have the obtain_structure.py file like following:

from modeller import *
from modeller.automodel import *    # Load the automodel class

log.verbose()
env = environ()

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

a = automodel(env, alnfile = 'alignment.ali',
              knowns = 'pl5t', sequence = 'plxd')
a.starting_model= 1
a.ending_model  = 1

#a.loop.starting_model = 1
#a.loop.ending_model   = 2
#a.loop.md_level       = refine.fast

a.make()

Above files are built based on instructions online. But when I used mod9v8 obtain_structure.py command, I got following error message:


                         MODELLER 9v8, 2010/04/21, r7145

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


                      Copyright(c) 1989-2010 Andrej Sali
                            All Rights Reserved

                             Written by A. Sali
                               with help from
           B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
                N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser,
                    R. Sanchez, B. Yerkovich, A. Badretdinov,
                      F. Melo, J.P. Overington, E. Feyfant
                 University of California, San Francisco, USA
                    Rockefeller University, New York, USA
                      Harvard University, Cambridge, USA
                   Imperial Cancer Research Fund, London, UK
              Birkbeck College, University of London, London, UK


Kind, OS, HostName, Kernel, Processor: 4, Linux karplus3 2.6.35.12-88.f c14.x86_64 x86_64
Date and time of compilation         : 2010/04/21 09:44:36
MODELLER executable type             : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2011/04/26 17:37:48

openf___224_> Open           $(LIB)/restyp.lib
openf___224_> Open           ${MODINSTALL9v8}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups:        2
openf___224_> Open           ${MODINSTALL9v8}/modlib/sstruc.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3234076    3158.277     3.084

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3234604    3158.793     3.085
openf___224_> Open           ${MODINSTALL9v8}/modlib/resdih.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3283204    3206.254     3.131
rdrdih__263_> Number of dihedral angle types         :        9
              Maximal number of dihedral angle optima:        3
              Dihedral angle names                   :  Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open           ${MODINSTALL9v 8}/modlib/radii.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3292444    3215.277     3.140
openf___224_> Open           ${MODINSTALL9v8}/modlib/radii14.lib
openf___224_> Open           ${MODINSTALL9v8}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes:  APBLE
openf___224_> Open           ${MODINSTALL9v8}/modlib/mnch.lib
rdclass_257_> Number of classes:        5
openf___224_> Open           ${MODINSTALL9v8}/modlib/mnch1.lib
openf___224_> Open           ${MODINSTALL9v8}/modlib/mnch2.lib
openf___224_> Open           ${MODINSTALL9v8}/modlib/mnch3.lib
openf___224_> Open           ${MODINSTALL9v8}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types:       21
openf___224_> Open           alignment.ali

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3303901    3226.466     3.151

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3305351    3227.882     3.152

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3308251    3230.714     3.155

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3369383    3290.413      3.213
parse_pir__E> Invalid PIR file header line: sequence:plxd
There should be 10 fields separated by colons, :
This line actually contains 2 fields.

I really do not know how to solve the problem. Could you give me some help on that? Thank you very much.

Best,

lqz