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

Eric Pettersen pett at cgl.ucsf.edu
Thu Sep 16 11:08:44 PDT 2010

Hi Christian,
	I'm happy you like Chimera enough to mis-use in in this way! :-)   
However, I don't think "rainbow" is the way to go here.  Rainbow only  
affects connected strings of residues.  For example, if you rainbow a  
protein system, waters and ligands will retain their original colors  
(and for your system, Chimera really has no way of knowing that your  
"residues" aren't peptide ligands).
	SInce you are creating your own PDB files anyway, what I suggest is  
that your put your "grouping info" into the bfactor field.  Then you  
can use the Render by Attribute tool (or the rangecolor command) to  
color your points based on their bfactor.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Sep 16, 2010, at 9:21 AM, Christian Schudoma wrote:

> 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
> wire-representation).
> 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 ;)
> Cheers,
> Christian
> ---
> Christian Schudoma, M.Sc.
> Ph.D. Student
> Bioinformatics Group
> Max Planck Institute of Molecular Plant Physiology
> Am Muehlenberg 1
> 14476 Potsdam-Golm
> Germany
> phone: +49 (331) 567-8624
> email: schudoma at mpimp-golm.mpg.de
> http://rloom.mpimp-golm.mpg.de
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20100916/35f40364/attachment.html>

More information about the Chimera-users mailing list