From: Peter Murray-R. <pm...@ca...> - 2003-09-18 22:30:28
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At 17:54 18/09/2003 +0200, Miguel wrote: >Peter, > >I went to make the 'small' change to Jmol ... and now I am confused :-) I'll try... > >>>RasMol/Chime render the positive y axis going down (and positive z > >>> axis > >>> going away from the user and into the screen) I haven't got Rasmol here so I can't vouch for the accuracy of this assertion > > Agreed > >RasMol has the following > -positive X goes to the right > -positive Y goes down > -positive Z goes away This describes RH axes... >Of course, when I flipped the y axis then the mouse behavior was backwards >... so I fixed that. "flipped" is not clear. If you simply changed +y to -y then the axes become LH and that is incorrect. If you want to change y ==> -y you must change another axis so the effect is a rotation. That could be (say x, y, z ==> x, -y, -z) >Then I tested the 'rotate commands' ... and they were broken too. So much >for my 'simple' change :-) > >That got me wondering about the RasMol 'rotate' command > >However, when you say: > rotate y <degrees> > >It is actually rotating as if the +Y axis is pointing upwards ... at least >that is what it looks like to me. > >rotate x <degrees> & rotate y <degrees> behaved as I expected. Rotate should rotate the molecule relative to screen axes. The sign of the rotation is critical. To determine that you must have ball and stick or spacefill showing. If your Y axis is down the screen and you apply a positive rotation I would expect the atoms nearest to you to rotate leftwards and the ones farthest away to rotate rightwards. This is a clockwise rotation about a Y axis down the screen. In some systems rotation is of the viewpoint, not the object. But that is uncommon in molecules. It can be tricky to do in some graphics libraries. I doubt that is the case with RasMOL which probably does all its own rotations >Now my brain is spinning ... but I don't know which axes it is spinning >around :-) > >Please advise. It will help you to get a small molecule which you understand. It will further help to make a physical molecular model. You can compare this with what happens on the screen. In all cases it must be superimposable with the screen molecule or you will have changed the chirality - not allowed. If you don't have models use an orange with 4 cocktail sticks and four atoms of different colours. Create a file for a molecule like HC(F)(Cl)Br which is a tetrahedron. If you don't have that the coordinates are 1 1 1 -1 -1 1 1 -1 -1 -1 1 -1 HTH >Miguel > > > > > >------------------------------------------------------- >This sf.net email is sponsored by:ThinkGeek >Welcome to geek heaven. >http://thinkgeek.com/sf >_______________________________________________ >Jmol-developers mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-developers |