Jan, what do you think is different about the Windows version of RasMol?it's a labeling issue (RasWin has a wrong Y axis labeling)
me too, therefore I inserted a
My confusion surrounding this issue is caused by the fact thatorientation
RasMol/Chime has the +Y axis pointing downwards. I find this
unnatural.
rotate z 180
in all my scripts (and there should be an rotate y 180, too), but I would be happy if this would be no longer necessary
I agree.Q: In the abstract, independent of any existing applications/scriptsthat
may exist, what do people think about this? Do you believe that the +Y'In the abstract', I am not too bothered about this. For me, a key part
axis should point upwards or downwards?
of visualising 3D structures on 2D screens is manually rotating them
using the mouse. So as long as I can rotate the structure so that +Y
points up, +X points right and +Z points to the viewer I am happy. That
said, it seems reasonable to 'open' molecular displays with +Y pointing
up and +X pointing to the right as this is the familiar convention (for
2D graphs etc).
it is easy for me to alter my script generating programs.
OK
Q: Given that there *are* existing applications and tutorials, what doyou
think we should do about this issue?I do not have a great deal of experience with these sorts of
RasMol/Chime scripts and tutorials. Given the inconsistencies and
variations in axis display noted above, I am not sure whether script
problems just relate to 'orientation' or to 'handedness'. Can anyone
clarify this?
I agree.
For all practical purposes, I have never written any scripts.
However, here is an example that makes sense to me: I have a protein and I want to hilite a particular region. To do so I change the color of that region, then position the molecule so that the region of interes is most visible.
If Jmol does not have the same initial orientation as Chime/RasMol, then my rotation commands are going to have to be different (although I am try to stay away from rotations ...)
I would prefer the default behaviour of Jmol to be as 'straightforward'
as possible. i.e. +X points to right. +Y points up, Z points out to the
user. I feel that script issues only involving 'orientation' should be
easy to deal with by changing the script (or options in Jmol).
OK
Script
issues involving handedness, if any exist, should *not* be accommodated
with options in Jmol.
I understand you to say that Jmol should not accomodate left-handed systems.
again, my agreement. Regards, Jan
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