Re: compare problems

[Alex Brown <>]

Hi, yet again.

I seem to have solved this particular problem.

Firstly, the INCLUDE command is not required.

Secondly, the structure files downloaded need to be renamed:

1bmdA.pdb -> 1bmd.pdb
4mdhA.pdb -> 4mdh.pdb
5mdhA.pdb -> 5mdh.pdb
7mdhA.pdb -> 7mdh.pdb

With these file name, the 'compare.top' script functions 'as is'. On my 
system, the family.mat is very slightly different from that in the 
tutorial, but that is probably due to processor rounding errors.

Cheers,

Alex.

On Tuesday, September 24, 2002, at 11:58  am, Alex Brown wrote:

> 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.