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 Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu 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@mpimp-golm.mpg.de http://rloom.mpimp-golm.mpg.de
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