Hi Ethan,
You need to put the files of PDB format in your own database or library.
The error message in get_structure*log shows that BALBES encountered
problems when it started to read your files to prepare the template models.
Thanks,
Fei
On Wed, 22 Jun 2011 10:26:26 -0700, Ethan Merritt
<[log in to unmask]> wrote:
> I would like to provide BALBES a set of locally-generated models
> to use as MR probes. These files contain SEQRES records and an
> arbitrary CRYST1 record
> CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1
> followed by the usual ATOM records.
>
> I created a subdirectory ./myprobes
> containing the models, and invoked BALBES using
>
> balbes -o `pwd` -f 182-3-h32.mtz -s Lm3759.pir -l myprobes/
>
> However, balbes apparently could not interpret the PDB files.
> In the top level output it says
> #-----------------------------------------------------------#
> # Model Database Analysis #
> #-----------------------------------------------------------#
> number of amino acids in the input sequence file is 113
> 4 structures found to be above 15% identity with the given sequence,
> Error message : no structure was found
>
>
>
> In process_details/get_structure*log it gave messages like:
>
> -- monomers start ----
> ===================================
> ====== structure 1 ========
> INFO: Nmod= 3 Percent of volume: 25.7
> Limit: 0.80
> ===================================
> ------ monomers ------
> ==:U__1___u
> ERR: Number of atoms = 0
> ERROR: in READPDB read user pdb file
> ===================================
> ====== structure 2 ========
> INFO: Nmod= 3 Percent of volume: 25.7
> Limit: 0.80
> ===================================
> ------ monomers ------
> ==:U__5___u
> ERR: Number of atoms = 0
> ERROR: in READPDB read user pdb file
>
> Do I need to pre-process the PDB files somehow before giving them
> to BALBES? I notice that its own database is not really in PDB format.
> I used BALBES_1.1.4 (Linux)
>
>
> Ethan
|