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 -- Timothy Driscoll em: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im: molvisions Washington St., Blacksburg, VA 24061 04-16-07. We will not forget you. ------------------------------------------------------------------------- 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
