[Chimera-users] Problem with Rainbow and "abnormal" PDB data
schudoma at mpimp-golm.mpg.de
Thu Sep 16 09:21:57 PDT 2010
Dear Chimera-devs and community,
I am "abusing" the 3D-rendering capabilities of Chimera to visualise 3D
coordinates that do not actually represent molecular data.
(Why do I do that? Because I love using Chimera for visualising
molecular data and I needed a quick way to display (+ rotate/zoom) 3D
data without hassle. I'm sure there are other solutions out there but I
found it easier to convert my data to PDB than find a decent tool or
code one myself.)
I convert my xyz coordinates into PDB-format, using Hydrogen atoms and
GLY as residue name (or, alternatively XXX - which wouldn't work
either). I use the residue index (resSeq) to identify groups of points
that belong together.
This of course results in a complete nonsense-"protein" (with
GLY-residues consisting of nothing but 100's of hydrogen atoms), which
is nevertheless in syntactically correct (I hope) PDB format and both
readable as well as displayable by Chimera (as a point cloud using
Now to the problem I encountered:
I would like to colour my "atoms" by their residue index.
I can colour the individual "atoms" manually, using Select-operations or
Ctrl-click and then the Color-menu. The Rainbow tool, however, does not
work to colour my point cloud. It simply doesn't do anything.
My question is, whether Rainbow performs some plausibility checking of
the data (and if so, then whether it is necessary to do that? It would
seem that Rainbow only needs to access either the residue, chain, or
model indices to do what it's supposed to do, i.e. to assign colour)?
Of course I am aware that my problem is kinda homemade and Rainbow works
fine for normal PDB structures. I am also not saying that Chimera's
buggy (although it seems to have a problem processing weird data in some
situations (Rainbow) but not in others (manual colouring)). However, I'd
like to understand why things don't work as expected ;)
Christian Schudoma, M.Sc.
Max Planck Institute of Molecular Plant Physiology
Am Muehlenberg 1
phone: +49 (331) 567-8624
email: schudoma at mpimp-golm.mpg.de
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