>> We also need to figure out what the center of rotation will be. How do >> you >> think we should choose the point that is the center of rotation for the >> entire set? > > I assume that when you mention the entire set you mean that all the > molecules will be considered (rather than a specific one). In that case > would it be reasonable to consider either > > a) the centroid of all the points (of all the molecules) or
Lets look at a few cases: Case 1 ------ Both molecules have atoms clustered around (0,0,0) The average of all the points is somewhere near (0,0,0) We center at the average of all the points. The result is that the two molecules are rendered with one directly on top of the other. Q: Is this a desirable thing? (I honestly don't know) Case 2 ------ Molecule A has atoms clustered around (1000,1000,1000) Molecule B has atoms clustered around (-1000,-1000,-1000) The average of all the points is somewhere near 0,0,0 We center at the average of all the points The result is that the molecules on-screen are very small ... two small clusters spread very far apart. Q: Do atom coordinates every get calculated so that they are located far away from (0,0,0)? I don't know. Q: Do people ever cut out pieces of a .pdb file just to look at section? Probably. > b) the center of the coordinate system that constitutes the current > viewport Not sure what you mean by this. Q: Are you saying that selecting a molecule means selecting a viewport? Q: If so, does this mean that the display 'shifts' when the user switches focus from one molecule to the next? Separately, and more imporantly ... Q: Is there any other molecular vision package that does this? Q: Is there any other molecular vision packate that does it *well* ? Miguel ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://productguide.itmanagersjournal.com/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
