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 ***************************
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