Hi Alicia, these are rounding errors. If you print the pairwise distances, which are stored in the b-factor column by the ColorByRMSD script, you will see some numbers which are not zero but close to zero (order of 1e-6). As soon as there is any real difference between the two conformations, the coloring should be correct. Yes, the script autoscales the colors depending on the range of deviations.
Cheers, Thomas Hersey, Alicia wrote, On 08/09/13 03:00: > Hi there, > > For anyone with experience using the ColorByRMSD script, I've used it to > compare two identical PDB structures and the result is a spectrum of > blues to reds, telling me there is discrepancy between the two > structures (when there shouldn't be?). Can anyone explain why this might > be happening, and if the script autoscales the colors depending on the > range of deviation in a given comparison? > > Thanks, > Alicia -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with <2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
