I'm guessing that MOL2 file does not include proper 3-letter PDB group
names in columns 61-63. Please send me a copy of the problem file.
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Hi Lochana,
We embed Jmol and redistribute Jmol.jar in our free StarBiochem application
(http://web.mit.edu/star/biochem/). The StarBiochem app has a user interface
that drives Jmol with scripts through the JmolViewer interface. Although the
scripting interface works and does most things we w
Chuck, question: JmolViewer extends JmolSimpleViewer, so how is it that
there is something in JmolSimpleViewer that is not in JmolViewer? Or is
"SimpleJmolViewer" your own class?
I regularly add aspects to JmolViewer that people need exposed. Do let me
know if that is the case. The point of using
Hi Bob,
I wrote my response from my memory of what we do and, unfortunately, I did not
look at our current codebase to see what we actually do. Now that I've done my
homework, you are absolutely correct in pointing out this flaw in my memory of
how to use Jmol. Whatever I was remembering abou
Hello Jmol community!
I am using Jmol in a web page with the javascript interface;
I belive that "select all" is the default rendering of the loaded molecule.
I would like, using the mouse and/or menu but not the console to be able
to unselect all and then toggle the selection state of individual
Hi Ted
1.
The popup menu has an entry named "set picking"
That should do what you want.
There is a "set picking" command too. If you look up the documentation for
that, you can see how it works.
2.
Given that the default is to start wirh all selected, maybe you want to
deselect all by includi
Hello Jmol community!
Is that even what you call them?
I am using Jmol in a web page with the javascript interface;
I needed to get the current value of a few state variables
to initialize the controls that I created to match the state
of the molecule loaded in the Jmol applet.
Currently, I do a
You can find ressources here :
http://chemapps.stolaf.edu/jmol/docs/#jmolmathread-onlyvariables
Le 31 janv. 2012 à 00:07, Ted Cohen a écrit :
> Hello Jmol community!
>
> Is that even what you call them?
>
> I am using Jmol in a web page with the javascript interface;
> I needed to get the curr
On Mon, January 30, 2012 16:44, Herráez Sánchez Ángel wrote:
> Hi Ted
>
> 1.
> The popup menu has an entry named "set picking"
> That should do what you want.
>
> There is a "set picking" command too. If you look up the documentation for
> that, you can see how it works.
>
> 2.
> Given that the de
> http://chemapps.stolaf.edu/jmol/docs/#jmolmathread-onlyvariables
and for other variables that are not on that list, check also the section on
Jmol Math and variables
Example:
var myslab = @{slab};
print myslab;
show myslab;
If you feel like improving my slab demo page, please do so. I can p
> Using the menus:
> 1) Jmol->Main Menu->Select->Selection Halos
> 2) Jmol->Main Menu->Select->None
> 3) Jmol->Main Menu->Set picking->Select Atom
Yes, of course.
Points 1 & 2 could be programmed into the page source if you don't want to do
them every time
jmolApplet(300, "load myFile.mol;selec
On Mon, Jan 30, 2012 at 5:07 PM, Ted Cohen wrote:
> Hello Jmol community!
>
> Is that even what you call them?
>
>
Is what even what you call what?
> I am using Jmol in a web page with the javascript interface;
> I needed to get the current value of a few state variables
> to initialize the con
Ted, maybe you are missing the significance of
http://chemapps.stolaf.edu/jmol/docs Sorry about that!
This is the official full all-inclusive description of Jmol scripting. Most
people, I think, load that page and then use their browser to search for
various items of interest. If you find somethi
Just a reminder -- please do not change subject lines. That breaks the
thread of a discussion.
Thanks.
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first wh
On Mon, January 30, 2012 18:04, Robert Hanson wrote:
> show state/"set spin" which will give you just one line to parse.
Very nice! I did not know that.
On Mon, January 30, 2012 17:13, Paul Pillot wrote:
> You can find ressources here :
> http://chemapps.stolaf.edu/jmol/docs/#jmolmathread-onlyvar
On Mon, January 30, 2012 18:11, Robert Hanson wrote:
> Ted, maybe you are missing the significance of
> http://chemapps.stolaf.edu/jmol/docs Sorry about that!
>
> This is the official full all-inclusive description of Jmol scripting. Most
> people, I think, load that page and then use their browse
Here is an example file.
Johannes
30.1.2012 17:03, Robert Hanson kirjoitti:
I'm guessing that MOL2 file does not include proper 3-letter PDB group
names in columns 61-63. Please send me a copy of the problem file.
Ah, right. Definitely not a protein!
On Mon, Jan 30, 2012 at 2:37 PM, johannes.per...@edumendo.fi <
johannes.per...@edumendo.fi> wrote:
> Here is an example file.
>
> Johannes
>
>
> 30.1.2012 17:03, Robert Hanson kirjoitti:
>
> I'm guessing that MOL2 file does not include proper 3-letter PDB gro
Ah, right! I see. Sure. I added hydrogen bond calculation outside of the
context of PDB files, and then I forgot to enable the menu item for that.
OK. This is fixed for Jmol 12.3.15 and 12.2.15.
See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
On Sat, Jan 28, 2012 at 12:57 AM, j
On Mon, Jan 30, 2012 at 6:17 PM, Ted Cohen wrote:
> On Mon, January 30, 2012 18:04, Robert Hanson wrote:
> > show state/"set spin" which will give you just one line to parse.
> Very nice! I did not know that.
>
> It appears that I can use jmolGetPropertyAs in the javascript
> interface to get
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