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 <[email protected]>: > 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! > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
