[Chimera-users] Problem with Rainbow and "abnormal" PDB data

Christian Schudoma 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.
Ph.D. Student

Bioinformatics Group
Max Planck Institute of Molecular Plant Physiology
Am Muehlenberg 1
14476 Potsdam-Golm

phone: +49 (331) 567-8624
email: schudoma at mpimp-golm.mpg.de

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