pgrupp/pdb_viewer

Viewer for PDB files using JavaFX GUI. Supports 3D view of any protein including cartoon view etc.

pdb_viewer's Issues

NPE in Parser

When parsing 5Z10 a NullPointerException is thrown. Needs investigation.

Unrealistic distance of bonds in quartenary structure

When more than one peptide is building the protein there are unrealistically long bonds generated for some residues following each other in the PDB file. When parsing a bond should not be set, if the two residues' center of mass are too far away.
Example PDB file for reproduction is 6B3R.

BLAST results are not removed when new file is loaded

When loading a new file the application does not reset any previously generated results of a BLAST query. This is desired behaviour and should be fixed.

Unknown amino acids not supported

An unknown amino acid type is not supported. The three letter code is UNK. Though it is not part of the standard it seems to be used, thus it should be supported. Example file is 6BPZ.

BoundingBoxes still appear when hiding C-beta atoms

When hiding the C-beta atoms bounding boxes for marked residues appear even for the hidden C-beta atoms. This is not desirable and should be fixed.