[ghemical-devel] ribbon bugfixes

Tommi Hassinen thassine@messi.uku.fi
Thu, 12 Sep 2002 13:56:00 +0300 (WET)


Hi all.

During this and the previous week I have added some improvements to the
peptide/protein ribbon object. The ribbons now are nicely coloured by the
secondary structure (helix/strand/loop).

I found out that previously, the ribbons have had chances to crash and/or
lock when created, but now it should be different. But still, the ribbons
are drawn for peptide/protein chains detected by the sequence builder
object, so there are still these (quite strict) requirements:

	1) the chains must be properly capped

		- in N-terminal with -NH3 or -NH2 groups.
		- in C-terminal with -COO or -COOH groups.

	2) the backbone must consist of proper peptide units:

			|
		      H-N
			|
		      R-C-R'
			|
			C=O
			|

	3) the minimum chain size is 3 residues.

There are no other requirements. For example manually drawn molecules are
equivalent to molecules read/imported from any file formats. All that
matters are the atoms and bonds that are in the file/system.

The most important application for ribbon is displaying imported Protein
Databank (PDB) files. Unfortunately, there are problems in many cases
where a PDB file is read in (using OpenBabel import) for ribbon display.
This is because the PDB file represents experimental data that might be
(and often is) incomplete so that the above requirements are not met (for
example, some part of a protein crystal might be disordered and/or mobile,
so the structure can only be partially solved -> there's a gap in the PDB
file -> no ribbon!).

For use with ribbons, I added an alternative PDB import function in popup
menu location "File/ExtraTools/ImportPDB..." that is designed to read in
"complete" PDB files (it ensures completeness for example by joining the
gaps in structure (and perhaps modifying the data)). This alternate PDB
reader is also slow since it probes the secondary structures; (small file
can be ~20 secs but a big one ~15 min!) so let it run for a while; it pro-
bably has not locked! So for displaying ribbons I recommend this alternate
PDB reader but beware - it might modify the data as I explained above
(also a dialog is displayed for users that warns about this).

	Tommi