Hi! I couldn't find this problem already posted:
until yesterday modeller8v0 was working perfectly without any problem.
Today I tried to create models using the same input files of yesterday and it
doesn't give me results anymore. In the .log file it is written:
Kind, OS, HostName, Kernel, Processor: 4, Linux job.saclay.cea.fr 2.6.9-1.667
i686
Date and time of compilation : 04/15/2005 15:55:19
MODELLER executable type : i386-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2005/05/30 15:54:25.936
runcmd______> alignment.append(align_codes=['1E6I', '1EQF', 'SNF2'],
atom_files=[], file='buonino3.ali', add_sequence=True,
(def)alignment_format='PIR', (def)remove_gaps=True, (def)close_file=True,
(def)rewind_file=False)
openf___224_> Open buonino3.ali
Dynamically allocated memory at amaxalignment [B,kB,MB]: 1919549
1874.560 1.831
Dynamically allocated memory at amaxalignment [B,kB,MB]: 1921249
1876.220 1.832
Dynamically allocated memory at amaxalignment [B,kB,MB]: 1924649
1879.540 1.835
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2134891
2084.854 2.036
Read the alignment from file : buonino3.ali
Total number of alignment positions: 119
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 1E6I 110 1 1E6I
2 1EQF 110 1 1EQF
3 SNF2 110 1 SNF2
runcmd______> alignment.check()
check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open 11 OLD SEQUENTIAL 1E6I
rdpdb___303E> No atoms were read from the specified input PDB file:
1) Possibly because an incorrect/non-existent PDB file is
specified.
2) Possibly because the segment is specified incorrectly in the
alignment file or by the variable MODEL_SEGMENT. That is,
the beginning residue number and/or chain id in MODEL_SEGMENT
may not be found in the input PDB file; MODEL_SEGMENT: 330:
A
To find out more, switch on maximal output by 'log.verbose()'
Dynamically allocated memory at amaxstructure [B,kB,MB]: 2135661
2085.606 2.037
openf5__224_> Open 11 OLD SEQUENTIAL 1E6I
rdpdb___303E> No atoms were read from the specified input PDB file:
1) Possibly because an incorrect/non-existent PDB file is
specified.
2) Possibly because the segment is specified incorrectly in the
alignment file or by the variable MODEL_SEGMENT. That is,
the beginning residue number and/or chain id in MODEL_SEGMENT
may not be found in the input PDB file; MODEL_SEGMENT: 330:
A
To find out more, switch on maximal output by 'log.verbose()'
rdabrk__288W> Protein not accepted: 1
69,1 Bot
Everything is the same: the alignment file, the template files are in the right
directory.
What could be the problem?
I post also the alignment file and the input file:
>P1;1E6I
structureX:1E6I:330 :A:439 :A:::-1.00:-1.00
G--PHDAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKM-EDFIYDARLVFN
NCRMYNG-ENTSYYKYANRLEKFFNNKVKEIP---E--YSHLID*
>P1;1EQF
structureX:1EQF:1382 :A:1491 :A:::-1.00:-1.00
MVT-LSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLY-PSREEFREHLELIVK
NSATYNGPK-HSLTQISQSMLDLCDEKLKEKEDKLARL------*
>P1;SNF2
structureX:SNF2:FIRST: :110 : :::-1.00:-1.00
ALDLYHFALNYENEAGRKLSDI--FLSKPSKALYPDYYMIIKYPVAFDNINTHIETLAY-NSLKETLQDFHLIFS
NARIYNT-EGSVVYEDSLELEKVVTKKYCEIMGDNSQL-----D*
~
from modeller.automodel import * # Load the automodel class
log.verbose() # request verbose output
env = environ() # create a new MODELLER environment to build this model in
# directories for input atom files
env.io.atom_files_directory = './:./atom_files'
a = automodel(env,
alnfile = 'buonino3.ali', # alignment filename
knowns = ('1E6I','1EQF'),
sequence = 'SNF2') # code of the target
a.starting_model= 1 # index of the first model
a.ending_model = 10 # index of the last model
a.make() # do the actual homology modelling
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