VMD User's Guide

}}# get the correct frame$compare frame $frame# compute the transformationset trans_mat [measure fit $compare $reference]# do the alignment$compare move $trans_mat# compute the RMSDset rmsd [measure rmsd $compare $reference]# print the RMSDputs "RMSD of $frame is $rmsd"To use this, load a molecule with an animation (for example, $VMDDIR/proteins/alanin.DCDfrom the VMD distribution). Then run print rmsd through time. Example output is shown here:vmd > print_rmsd_through_timeRMSD of 0 is 0.000000RMSD of 1 is 1.060704RMSD of 2 is 0.977208RMSD of 3 is 0.881330RMSD of 4 is 0.795466RMSD of 5 is 0.676938RMSD of 6 is 0.563725RMSD of 7 is 0.423108RMSD of 8 is 0.335384RMSD of 9 is 0.488800RMSD of 10 is 0.675662RMSD of 11 is 0.749352[...]11.5 VMD Script Commands for ColorsIn order to fine tune color parameters, one typically needs more sophisticated controls than thoseoffered in the GUI. For this reason, VMD provides a number of scripting level commands for coloraccess. These commands will be discussed in detail in chapter 8, but to give you a flavor for theiruse, here are a couple of examples that you may find useful right away. Most things can be donewith color [§8.3.4] and colorinfo [§8.3.5] commands.11.5.1 Changing the color scale definitionsSuppose that of the 1024 colors, the first 511 should be red, then 2 whites, and finally 511 blues.You can use the ‘color’ command to modify the color scale values accordingly.proc tricolor_scale {} {set color_start [colorinfo num]168