On Fri, 2002-11-15 at 23:20, mth wrote: > 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
I am also thinking of other schemes: *ask the user to pick an atom which will be the center of rotation. *ask the user to enter a coordinate. > > 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? Maybe we should add a new dialog with this features: -select a rotation scheme -fine rotations: do a rotation of x degree about a given axis (x, y, z or user input). From the abinit workshop I know that users are very interested in that kind of feature. Fabian > > 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 -- ********** Fabian Dortu Phone : 32-475-599268 e-mail : [EMAIL PROTECTED] ***********************************************
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