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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