[Biojava-l] BioJava

[Andreas Prlic]

Hi Michal,

If you look at the summary of the structure alignments, the alignment went well
> #1 cluster:1 eqr:17 rmsd:0.00 %id:17 gaps:0 score:102.00
and it superimposed your 17-residue test fragments perfectly.

The problem is that you got a weird residue naming in your input files
as is indicated by the output
> unknown amino acid CCC

so the BioJava PDB output method converts those groups to Hetam records:

HETATM    1  CA  CCC A   1      14.566  55.361  10.273     1     0
HETATM    2  CA  CCC A   2      26.928  51.739  16.185     1     0
HETATM    3  CA  CCC A   3      13.379  55.253   7.685     1     0
HETATM    4  CA  CCC A   4      18.626  45.916   1.163     1     0
...

I assume your viewer does not display this right? Set it to spacefill
mode and you will see the atoms....

To conclude, If you replace your input file with some real protein
data it will work fine....

Andreas




2008/12/26 Michal Lorenc <m.t.lorenc at wp.pl>:
> Hello Andreas,
> I tried to superpose two pdb files with BioJava (
> http://www.biojava.org/wiki/BioJava:CookBook:PDB:align ), but unfortunately
> it does not work with attached two pdb files.
>
> aligning centroid_template vs. centroid_target
> unknown amino acid CCC
> unknown amino acid CCC
> ....
> unknown amino acid CCC
> #1 cluster:1 eqr:17 rmsd:0.00 %id:17 gaps:0 score:102.00
> #2 cluster:1 eqr:17 rmsd:0.00 %id:17 gaps:0 score:102.00
> #3 cluster:1 eqr:17 rmsd:0.00 %id:17 gaps:0 score:102.00
> #4 cluster:1 eqr:17 rmsd:0.00 %id:17 gaps:0 score:102.00
> #5 cluster:1 eqr:17 rmsd:0.00 %id:17 gaps:0 score:102.00
> #6 cluster:1 eqr:17 rmsd:0.00 %id:17 gaps:0 score:102.00
> #7 cluster:1 eqr:17 rmsd:0.00 %id:17 gaps:0 score:102.00
> #8 cluster:1 eqr:17 rmsd:0.00 %id:17 gaps:0 score:102.00
>
>  0.194 -0.854 0.483
>  0.949 0.289 0.129
>  -0.250 0.433 0.866
> writing alignment to centroid_template_centroid_target.pdb
>
> Do you know how could I fix the problem?
>
> Thank you in advance.
>
> Best regards,
>
> Michal
>
> P.S. Happy New Year!
>