compare problems

[Alex Brown <>]

Hi, again.

Thanks to all those who answered my previous questions. I haven't had 
time to checkout the SEQUENCE_SEARCH suggestion, but if MODELLER takes 2 
hours or more to find a suitable template, perhaps a BLAST search of the 
PDB or ExPDB databases would be quicker.

Also, the MODELLER ftp server is up and running, and I have downloaded 
and looked at some of the files. In particular, I have downloaded the 
structure files associated with the TvLDH example.

This leads me on to my next problem - I have downloaded the file 
'compare.top' and the structure files 1bmdA.pdb, 4mdhA.pdb, 5mdhA.pdb 
and 7mdhA.pdb, along with TvLDH.ali. Running the 'compare.top' script 
produced the following (edited) .log file:

Multiple dynamic programming alignment (MALIGN):
  Residue-residue metric  : ${MODINSTALL6v2}/modlib//as1.sim.mat
  ALIGN_BLOCK             :            1
  Gap introduction penalty:    -900.0000
  Gap extension penalty   :     -50.0000
  Length of alignment     :          355
pdbnam__217W> Filename for PDB code not found:  1bmd
              Directories:  ./
              Extensions :   :.atm:.pdb:.ent:.crd
rdabrk__288W> Protein not accepted:        1
pdbnam__217W> Filename for PDB code not found:  4mdh
              Directories:  ./
              Extensions :   :.atm:.pdb:.ent:.crd
rdabrk__288W> Protein not accepted:        2
pdbnam__217W> Filename for PDB code not found:  5mdh
              Directories:  ./
              Extensions :   :.atm:.pdb:.ent:.crd
rdabrk__288W> Protein not accepted:        3
pdbnam__217W> Filename for PDB code not found:  7mdh
              Directories:  ./
              Extensions :   :.atm:.pdb:.ent:.crd
rdabrk__288W> Protein not accepted:        4
fndatmi_284E> Beginning atom index for a residue out of bounds:        
0        0
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at          finish [B,kB,MB]:     
14267969   13933.563    13.607
Starting time                                            : 2002/09/24  
11:50:17.110
Closing time                                             : 2002/09/24  
11:50:45.289
Total CPU time [seconds]                                 :      12.99

I edited the compare.top file, putting an INCLUDE command as the first 
line. This produced the following (again, edited) .log file:


Multiple dynamic programming alignment (MALIGN):
  Residue-residue metric  : ${MODINSTALL6v2}/modlib//as1.sim.mat
  ALIGN_BLOCK             :            1
  Gap introduction penalty:    -900.0000
  Gap extension penalty   :     -50.0000
  Length of alignment     :          355
fndatmi_284E> Beginning atom index for a residue out of bounds:        
0        0
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at          finish [B,kB,MB]:     
14267969   13933.563    13.607
Starting time                                            : 2002/09/24  
11:53:44.067
Closing time                                             : 2002/09/24  
11:53:59.605
Total CPU time [seconds]                                 :      13.67

Could someone please where the error is, and why, initially, the .pdb 
files are not seen.

I am running MODELLER on Mac OSX (Powerbook G4).

Thanks,

Alex.