From: Bob H. <ha...@st...> - 2005-06-05 03:53:20
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Right, I see. Well, all the pieces are there. You can experiment at http://www.stolaf.edu/people/hansonr/jmol/docs/examples/moveto.htm (when it comes back up; upgrade this weekend is taking longer than expected, it looks like) If I were you, I would load 1crn.pdb there, play around with commands, and then compare to chime. Yes, I believe the y axis is flipped, but that's it. Maybe a rotation difference. We should probably put up a table of differences between Chime and Jmol. That could be useful. In any case, I think all is there that you need. If you want, I can certainly add info in the script documentation or moveto.htm that helps Chime users. If you could look at slab and depth, that might be helpful. Is this the same implementation as Chime? Different? Here's the jmol implementation notes I have: slab 50; depth 0; # show the back half of the molecule slab 100;depth 50; # show the front half of the molecule slab 75; depth 25; # show middle 50% of the molecule slab 50;depth 50; # show a plane that is 1 pixel deep If I recall what you wanted to do was to write a script translator. That sounds really nice. Right now you just have to implement "view set" with all the individual commands. It's just that there isn't that exact command. Probably moveTo won't help you much, because it was implemented using Euler zyz angles. I would stick to rotate, translate, zoom, depth, and slab. Actually, the MOVE command is closest to view set: move The move command provides powerful animation capabilities. It allows you to specify rotations, zooming, and translations to be performed in a specified period of time. xRot, yRot, and zRot are rotations about the cartesian axes in degrees. Zoom specifies a zoom factor (there is a good chance this is not currently implemented properly) xTrans, yTrans, and zTrans are translations in the range -100 to 100. If you do not know what slab is, just put in a zero. see the slab command for more information. move [x-rotation] [y-rotation] [z-rotation] [zoom-factor] [x-translation] [y-translation] [z-translation] [slab-cutoff] [seconds-total] [move-frames-per-second]{default: 30} [maximum-acceleration]{default: 5} where [x-rotation] is the degrees of rotation about x -- (integer) [y-rotation] is the degrees of rotation about y -- (integer) [z-rotation] is the degrees of rotation about z -- (integer) [zoom-factor] is a scaling factor -- (integer) [x-translation] is the distance offset along x -- (integer) [y-translation] is the distance offset along y -- (integer) [z-translation] is the distance offset along z -- (integer) [slab-cutoff] is the cutoff for the slab display -- (integer) [seconds-total] is the amount of time to wait -- (decimal) [move-frames-per-second] is the frames per second to move -- (integer) [maximum-acceleration] is the maximum acceleration -- (integer) rotation order may be a problem there. You will have to check. basically, all rotations follow the right-hand rule, and the axis set is right-handed as well, with x right, y up, and z toward you. The order of rotation may not be what you want there. Bob Eric Martz wrote: >>> Further, I would have to round each value to the nearest integer. Yes, that's true for translate and zoom. Are the definitions the same for these? > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr |