modeller_usage@salilab.org Dear Modeller users, I need to model a homodimer from a homodimer templare. How my alignment file must look like? I mean I have problems with aminoacids numbers and chain names. How to solve this problems? I've attached all input files. Do I need to rename and renumber sequence or I can complete the task without it?

Respectively yours, Andrew

MODELLER 8v1, Jun 20, 2005 11:37am

PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS

Copyright(c) 1989-2005 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 Home 2.6.8-24-default i686 Date and time of compilation : 06/20/2005 12:25:12 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2006/11/18 01:06:28.018

openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/resdih.lib 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 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['mfzd', 'fzd1'], atom_files=[], file='fzd1.pir', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True)

openf___224_> Open fzd1.pir

Dynamically allocated memory at amaxalignment [B,kB,MB]: 2124923 2075.120 2.026

Dynamically allocated memory at amaxalignment [B,kB,MB]: 2126623 2076.780 2.028

Dynamically allocated memory at amaxalignment [B,kB,MB]: 2130023 2080.101 2.031

Dynamically allocated memory at amaxalignment [B,kB,MB]: 2136823 2086.741 2.038 openf5__224_> Open 13 OLD SEQUENTIAL mfzd.pdb rdpir___648E> Alignment sequence not found in PDB file: 1 mfzd.pdb