I have spoken with Tim off-line. *I* am the one who was confused, not Frieda & Tim.
>> the goal is to convert the output of Chime's 'view show' >> command into a set of orientation commands that Jmol >> understands, without user involvement. I did not understand the behavior of the chime 'view show' command. Tim explained that 'view show' reports results relative to the default center in Chime. That is, after loading any molecule, Chime reports the center of rotation as 0,0,0. All other centers of rotation are relative to that point. Actually, Frieda had explained this Chime behavior to me once before, but I had forgotton. >> the problem was that we had the center coords from Chime, but >> applying them in Jmol using 'centerAt boundbox' was not >> giving the expected results. > > That is because 'centerAt boundbox' was the wrong command. I was wrong ... centerAt boundbox <deltaX> <deltaY> <deltaZ> ... is exactly the right command > You don't want the center it relative to the boundbox, > you want to center > it at an absolute coordinate. They *do* want to center it relative to the boundbox ... because they are translating Chime scripts and the center coordinates reported by the Chime 'view set' command are relative to the center of the boundbox. >> we thought that 'centerAt boundbox' might not be working; >> in fact, it appears to be working just fine. BUT... you must >> switch the sign of the z center coordinate from Chime first. >> argh. <doh>. for lack of a nail... > > Now I am very confused ... ?!#@(*& Tim is correct. The problem with the sign on the Z coordinate results from the fact that the display coordinate system for RasMol/Chime is left-handed. (Note that while the display coordinat system is left-handed, rotations about the z-axis in RasMol/Chime are not left-handed ... they are the negative of left-handed). Jmol is consistently right-handed, so the sign of the deltaZ reported by Chime must be flipped in order to position the center of rotation at the same spot. Miguel ----- Open Source Molecular Visualization www.jmol.org [EMAIL PROTECTED] ----- ------------------------------------------------------- This SF.Net email is sponsored by the JBoss Inc. Get Certified Today Register for a JBoss Training Course. Free Certification Exam for All Training Attendees Through End of 2005. For more info visit: http://ads.osdn.com/?ad_idv28&alloc_id845&op=click _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
