Dear all,
firstly I would like to thanks to all by tips and answers about my last problem of stack problems. Thanks!
I am using the basic tutorial steps (1., 2., 3. , 4. , 5.) to "modeling based on a single template" with my sequence data:
- I get sucessful at searching for structures related at my sequence (Step 1), No problems!
- I do the "STEP 2 - selecting a template" and I find it using the same tips from the tutorial. No problems again;
- The problems is in the 'STEP 3 - aligning with the template". Because I have just the target code at the _aln.pos columm and it is missing the template code and its data in the cbp20-1h2v.pap result file (in this message).
Why ??? I see the "align2d_276_> ALIGN_BLOCK changed to 1" message at log file (at end of this message) but I did not find the main raison for it. There are an template and a target. So I think the ALIGN-BLOCK is 2.
I used the TOPOLOGY FILE = '/usr/lib/modeller7v7/modlib/top_heav.lib', but I am not sure that because there was not this command line at basic example. And if I run this script wihout this command line the Modeller tell me by warning that it missing in memory an topology library!
Can you help me ?
Best regards,
The cbp20-1h2v.pap result file is :
_aln.pos 10 20 30 40 50 60 cbp20 DHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARLLPEKLTIYTTLVGLLNAR _consrvd
_aln.p 70 80 90 100 110 120 130 cbp20 NYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCHVIAAPSMVAMFENFVSVTQEEDVPQV _consrvd
_aln.pos 140 150 160 170 180 190 200 cbp20 RRDWYVYAFLSSLPWVGKELYEKKDAEMDRIFANTESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCL _consrvd
_aln.pos 210 220 230 240 250 260 270 cbp20 WAQIQKLKKDRWQERHILRPYLAFDSILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEG _consrvd
_aln.pos 280 290 300 310 320 330 340 cbp20 PVMPGSHSVERFVIEENLHCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELFQLPAPPHI _consrvd
_aln.pos 350 360 370 380 390 400 cbp20 DVMYTTLLIELCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHHLSNFQFRWSWEDWSDC _consrvd
_aln.p 410 420 430 440 450 460 470 cbp20 LSQDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPSNPTCIYKYGDESSNSLPGHSVALCL _consrvd
_aln.pos 480 490 500 510 520 530 540 cbp20 AVAFKSKATNDEIFSILKDVPNFNPLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKL _consrvd
_aln.pos 550 560 570 580 590 600 610 cbp20 HVLRVMFEVWRNHPQMIAVLVDKMIRTQIVDCAAVANWIFSSELSRDFTRLFVWEILHSTIRKMNKHV _consrvd
_aln.pos 620 630 640 650 660 670 680 cbp20 LKIQKELEEAKIERLQEKVESAQSEQKNLFLVIFQRFIMILTEHLVRCETDGTSVLTPWYKNCIERLQ _consrvd
_aln.pos 690 700 710 720 730 740 cbp20 QIFLQHHQIIQQYMVTLENLLFTAELDPHILAVFQQFCALQA/EKLLKKSCTLYVGNLSFYTTEEQIY _consrvd
_aln.p 750 760 770 780 790 800 810 cbp20 ELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQY _consrvd
I have the follow sequence file:
>P1;cbp20 sequence:cbp20:::::::0.00: 0.00 MSLEEFDEVKYDHSTKRLDTPSRYLLRKARRNPNGLQELRESMKSSTIYVGNLSFYTSEE QIYELFSKCGTIKRIIMGLDRFKFTPCGFCFIIYSCPDEALNALKYLSDTKLDEKTITID LDPGFEDGRQFGRGKSGGQVSDELRFDFDASRGGFAIPFAERVGVPHSRFDNSSSQSNTN NYIPPPDAMGTFRPGFDEEREDDNYVPQ*
And my script file is :
SET OUTPUT_CONTROL = 1 1 1 1 1 SET ATOM_FILES_DIRECTORY = './:../atom_files' READ_MODEL FILE = '1H2V.pdb' READ_TOPOLOGY FILE = '/usr/lib/modeller7v7/modlib/top_heav.lib' SET ADD_SEQUENCE = on SEQUENCE_TO_ALI ALIGN_CODES = '1H2V' READ_ALIGNMENT FILE = 'cbp20levure.ali', ALIGN_CODES = 'cbp20', ADD_SEQUENCE = ON ALIGN2D WRITE_ALIGNMENT FILE='cbp20-1h2v.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='cbp20-1h2v.pap', ALIGNMENT_FORMAT = 'PAP'
And the LOG file is :
MODELLER 7v7, Sep 12, 2004 09:15pm
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2004 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, 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 santos.isima.fr 2.6.10-1.9_FC2 i686 Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2005/01/27 08:18:54.794
Dynamically allocated memory at amaxseq [B,kB,MB]: 69639 68.007 0.066 TOP_________> 2 2 SET ATOM_FILES_DIRECTORY = './:../atom_files'
TOP_________> 3 3 READ_MODEL FILE = '1H2V.pdb'
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files/1H2V.pdb
Dynamically allocated memory at amaxbnd [B,kB,MB]: 13862819 13537.909 13.221 openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files/1H2V.pdb rdatm___297_> Segments, residues, atoms: 2 815 6667 rdatm___298_> Segment: 1 29 C 790 C 5905 rdatm___298_> Segment: 2 33 Z 125 Z 762 TOP_________> 4 4 READ_TOPOLOGY FILE = '/usr/lib/modeller7v7/modlib/top_hea; v.lib'
openf5__224_> Open 11 OLD SEQUENTIAL /usr/lib/modeller7v7/modlib/top_heav.lib openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL7v7}/modlib/models.lib TOP_________> 5 5 SET ADD_SEQUENCE = ON
TOP_________> 6 6 SEQUENCE_TO_ALI ALIGN_CODES = '1H2V'
TOP_________> 7 7 READ_ALIGNMENT FILE = 'cbp20levure.ali', ALIGN_CODES = 'c; bp20', ADD_SEQUENCE = ON
openf5__224_> Open 20 OLD SEQUENTIAL cbp20levure.ali openf5__224_> Open 20 OLD SEQUENTIAL cbp20levure.ali
Read the alignment from file : cbp20levure.ali Total number of alignment positions: 815
# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 cbp20 815 2 1H2V undefined TOP_________> 8 8 ALIGN2D
Dynamically allocated memory at amaxbnd [B,kB,MB]: 31302189 30568.543 29.852 align2d_276_> ALIGN_BLOCK changed to 1. openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files/1H2V.pdb openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20
Pairwise dynamic programming alignment (ALIGN2D): Residue-residue metric : ${MODINSTALL7v7}/modlib//as1.sim.mat Diagonal : 100 Overhang : 0 Maximal gap length : 999999 Local alignment : F MATRIX_OFFSET (local aln): 0.0000 FIX_OFFSETS : 0.0 1000.0 2000.0 3000.0 4000.0 N_SUBOPT : 1 SUBOPT_OFFSET : 2.0000 Alignment block : 1 Gap introduction penalty : -900.0000 Gap extension penalty : -50.0000 Gap diagonal penalty : 0.0000 Structure gap penalties : 0.350 1.200 0.900 1.200 0.600 8.600 1.200 0.000 Length of alignment : 815 Score : -42490.0000 TOP_________> 9 9 WRITE_ALIGNMENT FILE ='cbp20-1h2v.ali', ALIGNMENT_FORMAT ; = 'PIR'
openf5__224_> Open 14 UNKNOWN SEQUENTIAL cbp20-1h2v.ali TOP_________> 10 10 WRITE_ALIGNMENT FILE ='cbp20-1h2v.pap', ALIGNMENT_FORMAT ; = 'PAP'
openf5__224_> Open 14 UNKNOWN SEQUENTIAL cbp20-1h2v.pap
Dynamically allocated memory at finish [B,kB,MB]: 31302189 30568.543 29.852 Starting time : 2005/01/27 08:18:54.794 Closing time : 2005/01/27 08:18:58.353 Total CPU time [seconds] : 3.47