Timothy Driscoll wrote: >hi, > >I am using an external data file to apply a roygb color scheme to a >set of atoms. a snippet from an example data file looks like this: > >1 -2.0 -1.0 -1.0 -0.0 >2 7.0 9.0 6.0 8.0 >3 8.0 18.0 4.0 15.0 >4 7.0 12.0 12.0 17.0 >5 0.0 0.0 0.0 0.0 >6 4.0 5.0 4.0 5.0 >7 5.0 6.0 5.0 6.0 >8 5.0 6.0 5.0 6.0 >9 0.0 0.0 0.0 0.0 >10 0.0 0.0 0.0 0.0 >11 0.0 0.0 0.0 0.0 >12 0.0 0.0 0.0 0.0 >13 3.0 3.0 5.0 6.0 >14 0.0 0.0 0.0 0.0 >15 9.0 11.0 4.0 6.0 >16 6.0 14.0 12.0 20.0 >17 0.0 0.0 0.0 0.0 >18 0.0 0.0 0.0 0.0 >19 -0.0 -0.0 -1.0 -1.0 >20 12.0 15.0 21.0 23.0 >21 11.0 14.0 18.0 21.0 > > >my Jmol script loads this file and colors atoms (column 1) by the >values in the last column (4). the values in column 4 range from -9 >to 31 for this particular file. > >the Jmol output, however, is almost completely yellow and green, with >a little blue and no red: > ><http://www.molvisions.com/temp/colorissue.jpg> > >(left panel). this seems odd; I expected a smearing of color. a >different data file, with values ranging from -3124 to 77334, gives >an entirely red structure (above url, right panel). > > >my hypothesis is that the range of values is too wide, and maybe this >would work a lot better if I binned them into 5-10 categories first. >perhaps even log-transform them. this will require a bit of work, >though, so I thought I would float it on the list first. can anyone >confirm this hypothesis? > > >thanks! > >tim > > first confirm that Jmol is treating your data correctly. What is it reporting for the data range? You could set this range yourself so as to allow the outlyers to "overflow" the red/blue range and get a better distribution around the middle.
I think to do this you just get your color scheme set up as you have and then use something like color property_X "myscheme" range 27 29 to adjust that. -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
