> > > Most of the animations come out well, very representative of test data. > But, I have a few runs though that the opendx program thinks it should > swell the size of the atom as build-up occurs. So, as the data runs > through opendx, the build-up occurs the same as the other runs (physical > position of the atoms is ok, color representation of the different elements > is ok) but the size of the atoms changes. I've changed the "AutoGlyph" > ratio several times, but it only produced varying scales of the "swelling" > atoms.
Sounds like AutoGlyph is determining the radii automatically .. which is not a good idea for this application. You want to give each atom an explicit (Van der Waal's) radius as a data component and set the parameters of Glyph so that the spheres are drawn to the correct size based on the the data value. (I believe that is, set the ratio = 1.0) You can then use the scale parameter to select a full space-filling representation (1.0) or something more appropriate for balls and sticks (0.3). At any rate, the correct relative sizes of the atoms will be maintained. The AddRadii module in my old CMSP package will assign radii based on atom type from an imported pdb or mol2 format file. It's also easy to just create a data component in OpenDX and set it to some value. Richard Gillilan MacCHESS Cornell
