As far as multiple molecular models go, the issues are - What is the user hoping to accomplish? Is it important that the original coordinate system be respected? Or it is more convenient that the molecules be auto-centered on the screen?
The answer: It depends on the user and the task they're performing. There are many use cases where the relative coordinate systems of two or more input structures needs to be respected in order to for the content to make any sense. And there are use cases where users would simply prefer that all molecules just be centered on the screen. Then there are use cases where it's more helpful for them to be systematically displaced relative to one another. And finally, there are those use cases where you're applying some systematic transform to align two or more molecules. The bottom line is that, to be generally useful, Jmol needs to be to flexible in the respect (separate camera/object matrices are critical). Default behavior is a tough decision, but given Jmol target usage, centering is probably okay. So far, I am not aware of any program that supports all of the above use cases with a fair amount of extra work. Most of the professional tools respect input coordinate systems whereas most of the educational toys don't. As far as origins go. There are two primary use cases: (1) where the origin is fixed [well changeable, but not moving the camera] (2) where the origin moves with the camera. PyMOL supports both, and Jmol probably should too, since they have different constituencies. #2 is easier for newbies, by pro's prefer #1. Is there an XY translation function in Jmol's user interface? Also, is there an mouse interface yet for controlling Z-axis slabbing? These two capabilities are critical for professional usage. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:[EMAIL PROTECTED] ------------------------------------------------------- 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
