Hi,
Just discovered, downloaded and spent a few hours playing with
Jmol-8/JmolApplet-8 and the ‘sneak preview’ of Jmol-10. ABSOLUTELY
BRILLIANT!
I have been tinkering with web-based educational materials using Chime for
several years but have been totally frustrated by inconsistent behaviour
with different browsers and lack of support for Linux. The JmolApplet has
already solved most of these problems – all those who have contributed to
Jmol development are to be commended.
The materials I have been working on have been mainly targeted at
pre-university level (AS and A2 level in UK edu-speak) and involve inorganic
crystal and metal structures as well as organic molecules and biopolymers.
All currently use .pdb format. In this context, I have the following wish
list for RasMol/Chime scripting and other options in the forthcoming
Jmol/JmolApplet releases.
1. set unitcell on/off
It would be good to be able to display the unit cell when crystallographic
data is present in .pdb files. As set axes and set boundbox are already
implemented I presume this would not be too difficult. In my experience, the
rendering of the unit cell in RasMol/Chime was imperfect, particularly when
it intersected atom spheres at the corners of a unit cell, so it would be
nice if this was done ‘properly’ in Jmol.
2. set connect false/save (and initscript parameter)
For complex structures RasMol and Chime usually ignore CONECT records in
.pdb files and use their own internal algorithms to determine bonds. This
means that structures with ‘unusual’ bond lengths, e.g. ionic and metal
lattices, may not display correctly even if the bonds are described by
CONECT records. Further explanation and details can be obtained from:
http://www.umass.edu/microbio/rasmol/rasbonds.htm
The workaround for this in RasMol 2.6 (not sure about RasMol 2.7) and Chime
2 is provided by the set connect false command which forces use of the
CONECT records. In addition Chime 2 has the set connect save command which
forces the plugin to show bonds for all CONECT records in the .pdb file,
while at the same time calculating bonds not specified in the CONECT records
in the usual manner. Set connect save can also be issued in the embed tag
which invokes Chime 2 using the initscript parameter. Initscript is required
to execute the command before the molecule is loaded.
It would be nice if the JmolApplet would implement set connect false/save
with initscript, or some equivalent mechanism, to achieve the display of
structures with ‘unusual’ and heterogeneous bond lengths.
3. scaled
Chime includes the scale3d embed tag. When the same scale3d value is used
for multiple structure windows on a page, the viewer can compare the
relative size of the structures. I find this very useful for visualising,
for example, trends in atomic/ionic/metallic radii and bond lengths.
4. Alternative units (pm and/or nm) for displaying distances (in addition to
Å)
In common with most molecular display programs, Jmol, RasMol & Chime use Å
as the unit of distance measurement. Although the Ångström is the ‘natural’
unit for bond lengths, SI units are recommended for pre-university students
in the UK. Hence these students tend to encounter bond lengths measured in
pm (or nm) in most textbooks, exam papers etc. I certainly don’t want to
start a long thread discussing the relative merits of different units or at
what point in their education students should be introduced to the Å.
However, from my point of view, it would be good to have some mechanism for
switching to different units (pm) for distance measurements, with perhaps Å
as the default.
Of course, I am also looking forward to all the protein rendering options
and other goodies promised for Jmol-10. Again, thanks for all your efforts.
Regards,
Geoff Rowland
[EMAIL PROTECTED]
-------------------------------------------------------
This SF.net email is sponsored by: SF.net Giveback Program.
Does SourceForge.net help you be more productive? Does it
help you create better code? SHARE THE LOVE, and help us help
YOU! Click Here: http://sourceforge.net/donate/
_______________________________________________
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users
