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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