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Problems reading in pdb template file



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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