Anyone know what pymol does? -Robin -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Miguel Sent: Friday, March 24, 2006 7:42 AM To: jmol-developers@lists.sourceforge.net Subject: Re: [Jmol-developers] Re: [Jmol-users] spin/rotate consolidation -- request for comments
> OK, Miguel, this is jmol-developers. [snip] >> I have some thoughts about the spin-rotate model. Since you are now familiar with the transformations that take place we should have a conversation. For some time I have wondered about the deficiencies of the current center/rotation/translation model. Basically, the translations seem to mess things up, as does changing the center of rotation. Jmol's behavior is different from Chime/RasMol ... and I seem to recall that Chime is different from RasMol. I take this as an indication that others have struggled with the same problem. The translation operations are fundamentally different ... and therefore fundamentally flawed. They are performed after all of the rotational transformations and (if I recall correctly) are actually done in terms of pixels. That is, they do not go through the same transformation pipeline as everything else. Here is my thought ... We should visualize the rotation of the molecule as though there were a robotic arm that was anchored at the origin. The arm has a universal joint at each end. One universal joint is anchored at the origin. The other universal joint is attached to the molecule. The arm is extendible in that its length can change. Length of the arm may be zero. The arm attaches to the molecule at the center of rotation of the molecule. If we move the center of rotation of the molecule, we: 1. hold the molcule still in space 2. detach the arm from the old center 3. reattach the arm at the new center of rotation. I don't think that we need any elbows in our arm. The arm and the molecule will never collide. The univeral joint on the arm and the extendible arm length mean that we can position the arm wherever we want in 3 space ... covering arbitrary translations. The universal joint at the molecule means that we can orient the molecule however we want ... covering orientations. We can detach the arm from one location and reattach it at another location while holding the molecule still and changing the arm length + angle ... covering changes in rotation center. This means that we can change the center of rotation of the molecule in a smooth manner, including incrementally sliding the rotation center from one spot to another, making for smooth animations. I think this is a good model. If it sounds good to you, then we should try to implement it. Miguel ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=k&kid0944&bid$1720&dat1642 _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid0944&bid$1720&dat1642 _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
