> Recently Eric Martz pointed out other flaws in Rockets -- the fact =20
> 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 =20
> 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. =20=
> 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-=20
strands cannot be ignored.
This is especially apparent in beta-barrels, where the strands wrap =20
around the barrel.
If you approximate the strands by a straight arrows, the strands are =20
bound to clash,
and the barrel looks more like a bundle of sticks than like a barrel.
(http://www.biochem.unizh.ch/biocinfo/bugReports/rockets.html, first =20
two images) The
example shown, Green fluorescent protein, PDB entry 1GFL, is a =20
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 =20
-The second problem are kinked helices, that is, two helices that are =20=
joined in such a way
that no non-helix-residues are located between the two helices. These =20=
as one single helix.
images 3 and 4. Example: bovine Rhodopsin, pdb entry 1F88. )
As long as the secondary structure definition is taken from the PDB-=20
file, this one
can be avoided by adjusting the Helix boundaries, deleting the =20
residue located at the kink
from the HELIX record, forcing the program to interpret the kinked =20
helix as two distinct helices.
For automatic recognition of such problems, one would have to test =20
for a marked change in the direction
of the helix axis as one goes from one end of the helix to the other.
Dr. Annemarie Honegger, Ph.D.
Z=FCrich University, Dept. of Biochemistry
Tel.: 41-44-635 55 62
Fax: 41-44-635 57 12