> http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1f8v > the JavaConsole reports WARNING! DANGER! z < 0! transformPoint()
This is the problem that I am trying to resolve. Jmol needs to calculate the default center of rotation. It then needs to calculate the radius to the outermost object that will ever be rendered ... I think I will start calling it the 'bounding sphere'. Currently, the unitcell is not participating in those calculations. When the unitcell gets rendered, the lines are getting drawn outside of the 'bounding sphere'. That is what generates the WARNING! message that the z coordinate is invalid. >>>>Q: Within the file formats, is there a way to specify the bonding >>>> that exists between cells? >>>the bounding box has not to be inside the unit cell >>Sorry, I do not know what you mean. > if you look at nearly every crystallographic protein PDB file (1dcc, > 3cro !), I looked at 3CRO and I see what you mean. I am only an amateur and may be mistaken, but ... Looking at the data file, I see that the atoms all have negative x and y coordinates: ATOM 5 O5* A A 1 -16.851 -5.543 74.981 But the unitcell data is all positive: CRYST1 49.200 47.600 61.700 90.00 109.50 90.00 P 21 >From my limited knowledge, the unitcell starts at the origin. Therefore, it sure looks like a file data error to me. Can someone more experienced please comment on this? > the command > set unitcell on > java.security.PrivilegedActionException: > java.lang.reflect.InvocationTargetException I do know know who is generating the PrivilegedActionException ... was this in the Applet? > set boundingbox on > compileError(cannot SET:boundingbox) The command is: set boundbox on not set boundingbox on Miguel ------------------------------------------------------- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
