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
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
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'
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