Re: [Jmol-users] rockets

Tue, 29 Aug 2006 06:05:02 -0700


Recently Eric Martz pointed out other flaws in Rockets -- the fact that 
sometime some of the planks comprising the sheet arrows cross collide. 
In response to that, I created a new class of rendering called 
"cartoonRockets" that can optionally replace rockets.

It seems to me both of you are onto the same thing -- that rockets do 
not necessarily faithfully represent the secondary structure of proteins.

I have just uploaded a modified JmolApplet.jar file that changes 
cartoonRockets in a way that removes those loops you are referring to.

So, what I suggest is that if this bothers you, use cartoonRockets. The 
way to do this is as follows:

set cartoonRockets true;
cartoons on;


As I see it, there are two different problems in rockets:

 - Beta-strands have an intrinsic curvature, which in longer beta-strands cannot be ignored.
This is especially apparent in beta-barrels, where the strands wrap around the barrel. 
If you approximate the strands by a straight arrows, the strands are bound to clash, 
and the barrel looks more like a bundle of sticks than like a barrel.
example shown, Green fluorescent protein, PDB entry 1GFL, is a relatively mild case,
in TonB (2GRX) the arrows almost go through the center of the barrel)

This problem is solved in cartoonRockets, as it allows the sheets to curve.

-The second problem are kinked helices, that is, two helices that are joined in such a way
that no non-helix-residues are located between the two helices. These are represented
as one single helix. 
 (http://www.biochem.unizh.ch/biocinfo/bugReports/rockets.html, images 3 and 4. Example: bovine Rhodopsin, pdb entry 1F88.  )
As long as the secondary structure definition is taken from the PDB-file, this one
can be avoided by adjusting the Helix boundaries, deleting the residue located at the kink
from the HELIX record, forcing the program to interpret the kinked helix as two distinct helices.
For automatic recognition of such problems, one would have to test for a marked change in the direction
of the helix axis as one goes from one end of the helix to the other.

                                                   Annemarie


________________________________________________________

Dr. Annemarie Honegger, Ph.D.
Zürich University, Dept. of Biochemistry
Winterthurerstr.190
CH-8057 Zürich
Switzerland

Tel.: 41-44-635 55 62
Fax: 41-44-635 57 12
_______________________________________________________



 

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