In the same folder as what?
J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN
Sent from my iPad
> On Jun 18, 2015, at 1:05 AM, Otis Rothenberger wrote:
>
> Phil,
>
> I'm at a loss other than saying that there is something inherent in Bob's
> JSmol/JSME page t
Sorry Phil, I wasn’t clear. I mean both pages were driven by the same
JSmol/JSME code. In other words, the problem is something on that Jmol/JME page
template.
I see the convenience of .js code that merges Jmol and JME, but I’ve always
used these as separate entities on a page. With advances i
We have "tour" scripts that use several moveto and rotate commands
during the script execution that take a few seconds each. We would like
to add a STOP button that once clicked would terminate the execution of
the tour script, even if it is in the middle of one of the moveto or
rotate steps.
It seems one of my former messages got lost.
Phil, this simplest code works fine:
var JSMEditor;
function jsmeOnLoad() {
if ( document.getElementById('jsmeContainer') ) {
JSMEditor = new JSApplet.JSME("jsmeContainer", {
"options" : "multipart,polarnitro,oldLook,atommovebutton",
Thanks
> On Jun 18, 2015, at 11:59 AM, Angel Herráez wrote:
>
> It seems one of my former messages got lost.
>
> Phil, this simplest code works fine:
>
>
>
>
>
>
> var JSMEditor;
> function jsmeOnLoad() {
> if ( document.getElementById('jsmeContainer') ) {
>JSMEditor = new JSApplet.
Hi Pshemak
probably the "immediate" option is what you need; that is adding an
exclamation sign before the command.
In your case,
!quit
or
!exit
(the difference is subtle, you need to investigate)
See
http://chemapps.stolaf.edu/jmol/docs/#immediate!
Yes, that is what it means.
On Tue, Jun 16, 2015 at 7:00 AM, Ward Poelmans wrote:
> Hi,
>
> I've got a question about the cut off for plotting molecular orbitals
> and isosurfaces. I want to plot my orbitals from a molden file and I
> noticed that molden and Jmol need a different cut off value t
Ah -- right -- Info.readyFunction is the one to use. Perhaps we should
abandon the readyCallback. I think JSmol uses it itself. By using it
yourself, you cancel code that JSmol needs to finalize the loading. (And
perhaps start more applets loading)
On Tue, Jun 16, 2015 at 12:40 PM, Angel Herráe
Eric, that's great. Are you utilizing Jmol's very powerful annotation
features? These allow you access to the full information in the PDB
validation suite, including close contacts, bad angles, and much more. It
uses the /val extension and gets its information from EBI.
$ load =1crn/val
*
Hello,
I'm using JmolData.jar to load a SMILES string and output the molecule in xyz
format:
java -jar "%JMOL_HOME%\JmolData.jar" -ion -s headless.spt $CC
where headless.spt consists of:
molunit = _arguments[1]
load @molunit
ml = molunit.length
xyzwrite = molunit[2][ml] + ".xyz"
writ
Thanks very much for this information, Bob!
My next big goal will be to move FirstGlance over from PDB format to
mmCIF format. I think it will require a lot of recoding of old code
(brought in from Protein Explorer) that parses components of the PDB header.
Regards, Eric
On 6/18/15 11:51 AM,
Jmol.___JmolVersion="14.3.15_2015.06.18"
bug fix: msCIF reader can hang if occupancy is not fractional
I will get a version out later today
On Wed, Jun 17, 2015 at 5:28 AM, wrote:
>
> Thanks Bob - the hanging issue is certainly fixed.
>
> I'm still seeing render errorjava.lang.NullPointerExc
I have increased the width of the JSME applet to be 350, even if I do like
squares. :)
Thanks, Angel.
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Jmol is not set up to load arguments into -s headless.spt
While that is an interesting option, it's just not there. I think the thing
to do is use -J instead of -s. This will run an in-line script, which can
then call your headless.spt script with a parameter:
java -jar "%JMOL_HOME%\JmolData.jar"
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