Hi Modellers!
I have the pdb format problem.
I have the same problem with Stephane Coillet-Matillon's error written
at 19 Mar 2002.
Eric Feyfant replied it was a chain identifier
problem.
" I corrected Stephane error. It
was a chain identifier problem. The chain was specified in the pdb but not in
the top file, and Modeler could not
extrapolate.
Eric"
But I don't know how to correct this problem.
How to solve this problem?
Thanks,
Ahrim
The error messages is like this
" Read the alignment from
file : acc_ipn1.ali
Total number of
alignment positions: 375
# Code
#_Res #_Segm PDB_code
Name
-------------------------------------------------------------------------------
1 1QJF
331 1
1QJF
2
ACCO 314
1 ACCO
unknown
TOP_________> 121 107
CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF
COMMAND
openf5__224_> Open 11
OLD SEQUENTIAL ./1QJF.pdb
rdpdb___303E> No atoms were read
from the specified input PDB
file:
1) Possibly because an incorrect/non-existent PDB file is
specif
ied.
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:
331
0
For alignment entry:
1
recover____E> ERROR_STATUS >=
STOP_ON_ERROR:
1 1
"
YOO, AHRIM
Process System Lab.
Department of Chemical
Engineering, Korea
University
---------------------------------------------------------------------------------------
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