The analysis of the final results from Blob is performed by the program Hits. Invoking Hits results in the quite lengthy error message:
| USAGE: hits | -r[required] Cluster Radius |
| -d[required] Data File | |
| -n[optional] N Hits Save | |
| -N[optional] Name | |
| -x[optional] Xray File | |
| -f[optional] PDB Format | |
| -k[optional] Key Word | |
| -m[optional] RMSD Matrix | |
| -i[optional] Iso File | |
| -g[optional] Space Group | |
| -H[optional] Hydrogens | |
| -h[optional] N Histogram Bins | |
| -b[optional] EBest | |
| -s[optional] EStep | |
| -X[optional] Xray | |
| -a[optional] Blob Alpha | |
| -C[optional] Blob C | |
| -W[optional] Blob Weight | |
| -L[optional] Blob Limit |
I use this program for lots of different tasks, and as a result it looks a little overwhelming (actually I am quite proud of it). There are only two required parameters -r and -d. Thus a minimally correct invocation of Hits would look like
| Hits -r 2.0 -d ZZZ.blb |
The -r option specifies the rms deviation cutoff used for clustering (in Å). The -d specifies the file containing the final results from Blob. I stress that the file ZZZ.blb is the same file specified as the output (-o option) file for Blob. That seems easy enough but there are a few other options worth mentioning.
First I am sure you would like to get some single output files. You can do this with the -n option. The command
| Hits -r 2.0 -d ZZZ.blb -n 7 |
would save the results from the seven best scoring clusters. The results would be written to the files hit001.pdb .... hit007.pdb with hit00n.pdb containing the position and orientation of the molecule with the best score from cluster n. Also if you use the -n option you should also consider using the -f option which allows you to tell Hits what the atom format is. This option will allow you to get information about the scores for each atom in the output. Basically, the atom format should be the same as that specified by the OUTPUT_FORMAT record in the parameter file (see section 3). See Section 8 for details concerning atom formats.
If you want to compare the positions in ZZZ.blb to some pre-determined position of your molecule the -x option will do the trick. The command
| Hits -r 2.0 -d ZZZ.blb -x xray.pdb |
will compare each of the positions in the file ZZZ.blb to the position in xray.pdb. You should be careful that the atoms of xray.pdb are ordered exactly as those in the file ZZZ.blb.