Hi,
I'm quite new to using MODELLER and am having
difficulties reading in a pdb template file.
Judging from the log file, I've been able to read in
the A chain of 1hzx, bovine rhodopsen, but later get a
complaint that no atoms were read from the specified
file. Can someone please give a hint as to what the
problem is? Below is my top file and the relevant
output from the log file.
Thanks,
Michael Moser
INCLUDE
SET OUTPUT_CONTROL = 1 1 1 1 0
SET ALNFILE = 'protstruct3.ali'
SET KNOWNS = '1hzx'
READ_MODEL FILE = '1hzx', MODEL_SEGMENT = 'FIRST:A'
'LAST:A'
SET SEQUENCE = 'jegA'
SET ATOM_FILES_DIRECTORY = './'
SET STARTING_MODEL= 1
SET ENDING_MODEL = 1
CALL ROUTINE = 'model' # do homology
modelling
TOP_________> 107 707 READ_MODEL FILE = '1hzx',
MODEL_SEGMENT = 'FIRST:A' 'LAST:A'
openf5__224_> Open 11 OLD SEQUENTIAL
./1hzx.atm
openf5__224_> Open 11 OLD SEQUENTIAL
./1hzx.atm
rdatm___297_> Segments, residues, atoms: 1
340 2681
rdatm___298_> Segment: 1 1 A 1 A
2681
TOP_________> 108 708 SET SEQUENCE = 'jegA'
.
.
.
.
Read the alignment from file : protstruct3.ali
Total number of alignment positions: 381
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 1hzx 348 1 1hzx
2 jegA 371 1 jegA unknown
TOP_________> 122 107 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open 11 OLD SEQUENTIAL
./1hzx.atm
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 TOP
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: 1:
To find out more, switch on maximal
output by 'SET OUTPUT_CONTROL = 1 1 1 1 2'
rdabrk__288W> Protein not accepted: 1
rdabrk__290E> Number of residues in the alignment and
pdb files are different: 348 0
For alignment entry: 1
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1
1
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