> I have tried the unit-cell enabled Jmol applet on a number of structures
> and it works well. It actually draws the unit cell in the 'right' place
> (unlike Chime and RasMol 2.6, but like OpenRasMol 2.7).
Glad to receive confirmation that the orientation is correct.
I didn't know that Chime/RasMol was wrong. I actually looked at the RasMol
2.6 source code, but could not understand the calculations ... in large
part because the scaling and translation to screen coordinates is all
taking place in the same function ... too much hair.
So Egon was good enough to do the initial implementation of the
transformation to cartesian coordinates.
> Also, if there
> are atoms at the corners of the unit cell, it correctly handles the
> intersection of the unit cell 'edges' and the atom spheres. You have
> certainly fulfilled the basic objective of a (correctly working!) Chime
> alternative with respect to this function.
Very good.
> The unit cell is a little faint. Would it be possible to render it with
> a thicker line or provide an option to this?
It may not be obvious, but the current rendering has the a,b,c edges
rendered as solid lines and the other edges rendered as dotted lines ...
that is part of the reason why they are so faint.
I plan to add support for user-specified widths to unitcell, boundbox, and
axes, as in:
set unitcell 0.1
set boundbox 0.1
set axes 0.05
These numbers will specify the radius in angstroms and will be analogous to
wireframe on/off/{size}
coloring will be handled the same way
color unitcell lemonchiffon
color boundbox lightgoldenrodyellow
color axes midnightblue
Note that this is *NOT* operational yet ... it is what I plan to do.
Q: Should the a,b,c legs be rendered differently from the others?
Q: They could pretty easily have a conical arrowhead ... would that be
useful?
Q: Should the origin be identified specially?
> The a, b, c, alpha, beta, gamma, info display is useful but I'm not
> quite sure as to the best place to put it.
I put it there for testing purposes. My plan was to take it away. If you
are building a web app it will be easy to display this information
elsewhere. Note, however, that Pat said that he liked it there.
> A few of my .pdb files didn't initially display with the Jmol Applet. It
> turned out that this was because I had used negative atom numbers for
> additional 'dummy' atoms I had added to the structures to define the
> corners of the unit cell. Apparently Jmol does not like these.
Hmmm ... I am surprised ...
> I have
> not yet checked whether negative atom numbers are allowed by the
> official pdb spec, but they certainly were tolerated by RasMol/Chime. I
> guess this won't crop up very often but just in case...
The pdb spec *does* allow negative numbers. And I thought that Jmol was
doing a good job of handling them.
Please send me a sample .pdb file that fails (preferably one that also has
a unitcell).
> I hope to stick some of these structures on a website somewhere in the
> near future so that you can look at them and I don't have to write so
> much :-)
Good!
Miguel
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