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
Attachment:
fzd1.log
Description: Binary data
Attachment:
fzd1.pir
Description: Binary data
Attachment:
fzd1.py
Description: Binary data
Attachment:
mfzd.pdb
Description: Protein Databank data