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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