In jmol the center of the molecule is the point about which the molecule is rotated.
Currently the center is the geometric center of the molecule based upon the cartesian coordinates stored in the file. That is, the center x coordinate is the average of the minimum x coordinate and maximum x coordinate in the file. y and z are the same. Note that this is somewhat arbitrary ... if the molecule coordinates are rotated file, then you will get a different center. It is probably not an important point, but as I am working on the code I am wondering whether or not this is the best definition. Three other ideas come to mind: 1. the center of gravity of the molecule (using atomic weights) 2. the unweighted "center of gravity" (all atoms weigh the same) 3. the center point of the smallest sphere which would enclose the molecule As I write this, I realize that these points would also change depending upon the orientation of the atoms in the file. So maybe it doesn't matter. What do you think? Miguel ------------------------------------------------------- This sf.net email is sponsored by: To learn the basics of securing your web site with SSL, click here to get a FREE TRIAL of a Thawte Server Certificate: http://www.gothawte.com/rd524.html _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
