VMD User's Guide

The last example shows how to set the beta field. This is useful because one of the coloringmethods is ’Beta’, which uses the beta values to color the molecule according to the current colorscale. (This can also be done with the occupancy field.) Thus redefining the beta values allows youto color the molecules based on your own definition. One useful example is to color the moleculebased on the distance from a specific point (for this case, coloring a poliovirus protomer based onits distance to the center of the virus (0, 0, 0) helps bring out the surface features).proc betacolor_distance {sel point} {# get the coordinatesforeach coord [$sel get {x y z}] {# get the distance and put it in the "newbeta" listset dist [veclength2 [vecsub $coord $point]]lappend newbeta $dist}# set the beta term$sel set beta $newbeta}And here’s one way to use it:# load pdb2plv.ent using anonymous ftp to the PDBvmd > mol new 2plvvmd > set sel [atomselect top all]vmd > betacolor_distance $sel {0 0 0}Then go to the graphics menu and set the ’Coloring Method’ to ’Beta’.11.4 RMS Fit and AlignmentWhen one has two similar structures, one often wants to compare them. What’s the differencebetween two X-ray structures? How much did the structure change during a simulation? Toanswer these questions, you must first figure out how to compare two structures, which usuallymeans that you must find the root mean square deviation (RMSD).Formally, given N atom positions from structure x and the corresponding N atoms from structurey with a weighting factor w (i), the RMSD is defined as:[∑ Ni=1RMSD (N; x, y) =w i‖x i −y i ‖ 2N ∑ Ni=1 w iUsing this equation by itself probably won’t give you the answer you are looking for. Imaginetwo identical structures offset by some distance. The RMSD should be 0, but the offset preventsthat from happening. What you really want is the minimum RMSD between two given structures;the best fit. There are many ways to do this, but for VMD we have implemented the method ofKabsch (Acta Cryst. (1978) A34, 827-828 or see file Measure.C in the VMD source code). Thisalgorithm computes the transformation, needed to move one structure onto another in order tominimize the RMSD.With the mathematical prerequisites behind us, we still need to be able to specify how to choosethe atoms to compare. If you want to compare all the atoms in both structures, and they both164] 12