At 08:25 AM 8/27/96 +0100, Alan Arnold wrote:
Greetings,
for those kind souls with a few spare minutes and a
chime-compatible browser, please check out
save the html source and explain to me why the embedded
application/x-spt
script (shamelessly transmogrified from MDL's chime scripting example)
doesn't work as expected.
This was to be prototype for some 'live' unit cells for some common
ceramic
crystal structures. I had hoped that it would display a CsCl unit
cell
showing both cell outlines and Cs-Cl connections as a visual aid, and
when
the script buttons were pressed, cpk shpheres of the appropriate sizes
would be displayed separately for Cl, Cs, ions then both together.
Doesn't
seem to work with NS 3.0 on my Mac on NS 3.0 for Win95. The cell
outlines
and 'bonds' are there (yay!!) but I don't seem to be able to get any
cpk
display :-(
I am not sure what the problem you are seeing is. When I visit your page the initial display is as I would expect from your embed tags for the chime plugin displaying the structure, and for the 4 chime buttons. I even tested your page with the new SGI version of Chime and it looks and works great. Your main structure embed tag: <<embed border=0 src="CsCl.mol" ALT="CsCl" align=abscenter width=400 bgcolor=#ffffff height=400 spiny=360 startspin=true name="CsCl" display3D=wireframe palette=foreground > The above is the embed that you are using, and everything you specify here is being displayed 'correctly' when I view your page. As far as the rasmol scripts (application/x-spt) embed tags which invoke 4 Chime 'buttons'... These scripts also work as I would expect them to. Rasmol (and chime) do not have a 'default' atom radii for 'spacefill' models, if none is specified after the 'spacefill' command than Van der Waals radii are used. The way you are specifying the radius after the spacefill commands ('spacefill ###') is correct for specifying a custom radius. (an example of one of your Rasmol scripts, this one attached to your Chime button "Display wireframe" "select all spacefill off wireframe on # only select (atomno>=1) and (atomno<<=8) colour atoms green spacefill 1.03 # select (atomno=9) colour atoms blue spacefill 0.732 " The above script (and your others) work exactly as I would expect. I will mention that in your initial 'structure' embed tag you can add a 'script="whatever rasmol script you want" ' argument to init your structure display with whatever specific rasmol commands you would like. For example you could use script= and the above script (in quotes) for your initializing rasmol script. You can also separate lines with '|' or ';' instead of hard carriage returns. (i.e. script="select all;spacefill off;wireframe on; select (atomno>=1) and atomno<<=8);colour atoms green;spacefill 1.03; select (atomno=9);colour atoms blue;spacefill 0.732"
The weird cpk scaling factors are my attempt to force the Cl and Cs
spheres
about the right size. I need a way of preventing the user from
displaying
as cpk in chime with inappropriate default atom radii (Where are the
default sphere sizes hidden in the chime plug-in?)
As I indicated above Rasmol and Chime both use Van der Waals radii when none is specified in the spacefill command. There is no default for the 'spacefill' command.
On a related note, can someone please point me in the direction of the
specifications for MDL's .mol file format?
(following extract from mail message from David Hughes of MDL) "CTfile Formats" is in Adobe Acrobat PDF format, suitable for reading by Adobe's Acrobat Reader (a free license for the Adobe Acrobat Reader can be obtained from Adobe's site.) You can download a copy of "CTfile Formats" from http://www.mdli.com/fileformats.html; this page also provides a link to Adobe's.
Any suggestions for the most
convenient file format to use as chime input for small inorganics of
this
type - in particular, do any formats allow user-defined atom radii?
Of course, if anyone has already done this before, I'd be every pleased
to
be further enlightened...
many thanks for listening.
Hope I have been of *some* help. -Tim
----
Alan Arnold, School of Chemistry, University College (UNSW)
Australian Defence Force Academy, CANBERRA ACT 2600 Australia
voice:+61 6 268 8080 fax:+61 6 268 8002 e-mail: apa@adfa.oz.au
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