> > 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.
Sorry...wasn't clear in the first case, there are actually multiple origins/centers, one for each object, and all objects rotate about their own -- so that you can inspect equivalent rotations of different side-by-side object. BTW PyMOL doesn't even support this yet, but some other tools do. In the second case, the objects share a center/origin, they've just been superimposed via some trans. matrix. > 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. Inserting a single 3x3 or 4x4 transformation into the pipeline shouldn't have that drastic of an impact and surely at least one of these already exists? You're not changing original model coordinates every time you rotate are you? The efficiency trick here is to precombine all of your operations upfront so that you only ever need to apply one single 4x4 to any input coordinate (and one single 3x3 to any input normal). > > Is there an XY translation function in Jmol's user interface? > > Yes. [snip] (NOTE: Doesn't work in all cases...why?) How about a graphical mouse quick help function? (gee wiz, who I am to talk -- PyMOL doesn't even have that!) > > 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 used to think this way until I added scroll-wheel slabbing into PyMOL... > > 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. Apples & oranges. PyMOL is a full-blown large-footprint application with no Java/ActiveX plugin yet. So at this point, pro's don't have a good tool for browsers. Jmol could be that tool... > 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. That's great, but I'd like to see Jmol eventually become economically self-sufficient just like PyMOL. In order to reach that point, Jmol must meet needs in biotech and pharma as well needs in educational settings. Considering that many students eventually become professionals, why not train them on a tool they can use in the real world? Also, I don't think either Jmol or PyMOL should dispense with one class of users -- but defaults is one thing and underlying capablities is another. I grant that Jmol defaults should be novice-oriented, and that's where early efforts should go, but when it comes to capabilities there's no reason to artifically limit yourself or your code. Cheers, Warren ------------------------------------------------------- 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
