On Thu, Oct 22, 2009 at 10:13 AM, Jason Grout <[email protected]> wrote: > > Bill Page wrote: >> The optional labeled axes in jmol 3-d graphics is a nice addition but >> take a look at, for example: >> >> line3d([(0,0,0), (-3,4,-5),(3,4,-5),(3,-4,5)]) >> >> In the 4.1.2 notebook. Right-click the image and turn on Style/Axes. >> Notice how the diagonal line does not appear to start at where you >> would expect the origin to be. The origin appears to be displaced a >> little along the Y-axes. Both the X and Y axes appear to extend beyond >> the box. Not too serious but is this a known problem? > > > Yes. The axes you turn on are centered in the picture, but do not > correspond to data coordinates. > > The underlying reason has to do with some fiddling that happens with > rescaling things so that to jmol, everything appears to be in a box > between [-1..1] (or something like that). The axes appear at the jmol
The motivation for using rescaling things and *not* using jmol coordinates, is that things go totally to hell if we use jmol coordinates. E.g., in math it makes perfect sense to say draw something where the x and y axis span a range of say 10^(-16), or to draw a sphere of radius 10^(-10), etc. If you do that with jmol coordinates, disaster occurs, since everything is floating point (??). So what happens now is that Sage maps its own scene to something like [-1,1] and jmol then renders it all nicely. I was the one who wrote the code so that this mapping is used, since I got very frustrated with jmol seriously corrupted images. You can understand why jmol wouldn't care about uses funny scales (like an x-axis range of 10^(-16)), because jmol is a program for visualizing molecules after all! > origin, but because we have scaled and translated things before sending > it to jmol, our origin may not correspond with the jmol origin. > > There is a trac ticket about this. Sorry, trac was crapping out again. I think we should move trac to run through apache not in a virtual machine. I may try to hire somebody to professionally maintain this, since our trac infrastructure being rock solid is so important. I have a little bit of Sage Foundation money that could be used for this... William --~--~---------~--~----~------------~-------~--~----~ To post to this group, send an email to [email protected] To unsubscribe from this group, send an email to [email protected] For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org -~----------~----~----~----~------~----~------~--~---
