Align pdb sequences using python and Modeller
Usage:
./align_pdb_seq.py pdb1 pdb2 [...]
Example output:
$ ./align_pdb_seq.py 148l.pdb 2lcb.pdb
MODELLER 9.16, 2016/01/07, r10745
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2016 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
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 mantrisse 3.16.0-4-amd64 x86_64
Date and time of compilation : 2016/01/07 09:23:18
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2016/09/06 12:36:19
SALIGN_____> adding the next group to the alignment; iteration 1
_aln.pos 10 20 30 40 50 60
148l MNIFEMLRIDEGLRLKIYKDTEGYYEIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFN
2lcb MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFN
_consrvd ************************* ******************************************
_aln.p 70 80 90 100 110 120 130
148l QDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKS
2lcb QDVDAAVRGILRNAKLKPVYDSLDAVRRAAAINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKS
_consrvd ****************************** *************************************
_aln.pos 140 150 160
148l RWYNQTPNRAKRVITTFRTGTWDAYKN/A
2lcb RWYNQTPNRAKRVITTFRTGTWDAYKN-L
_consrvd ***************************