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.fc14.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 ${MODINSTALL9v8}/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