Warren wrote: > 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.
Why of course! The answer is ... it depends ;-) > 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. OK > And there are use cases where users would simply prefer > that all molecules just be centered on the screen. OK > 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. It seems that these two cases are the same. It is just that the first one has a simpler transform ... translation only. > Default behavior is a tough decision, but given Jmol target usage, > centering is probably okay. That makes sense to me. > 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. OK > 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. Jmol has a very simple model of the camera. It is on the positive Z axis, looking at the origin. This has allowed me to simplify (and speed up) many of the calculations. I don't think we can change that ... just the thought of it makes me break out into a cold sweat. > Is there an XY translation function in Jmol's user interface? Yes. Ctrl-right drag for multi-button mice (RasMol/Chime compatible) OR shift dbl-click-drag for the 'button-challenged' members of the OSX community. > Also, is > there an mouse interface yet for controlling Z-axis slabbing? No. I feel that slabbing is too complicated a function to be controlled by a simple mouse gesture. I think that it would be more appropriate for to have a GUI control ... like a double-slider, with one for the back and one or the front > These two capabilities are critical for professional usage. I certainly don't have anything against professionals. With that said ... It seems to me that the professionals already have good tools ... like PyMOL. I think that Jmol's target audience is students and novices ... who don't have anything else. It is for building tutorials and scripted storyboards that explain things. Since I am neither a chemist nor an educator, it is still not clear to me what scenerios would require loading multiple models. Miguel ------------------------------------------------------- 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
