0.0 // default is 14.0
>
> see
>
> http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.6_2013.09.09.zip (very slowly
> uploading at 37 KB/s from this ACS meeting WIFI -- hopefully will complete
> in 20 minutes time.)
>
>
>
> On Mon, Sep 9, 2013 at 10:28 AM, Martin Guetlein
&g
set drawFontSize x.y
>
> work for you?
>
>
>
>
>
> On Mon, Sep 9, 2013 at 8:46 AM, Martin Guetlein
> wrote:
>>
>> Hi,
>>
>> I just run into this issue wants again, I really would like to
>> enlarged the bounding box fontsize.
>> Is there
, Sep 8, 2011 at 7:07 PM, Robert Hanson wrote:
>
>
> On Thu, Sep 8, 2011 at 11:50 AM, Martin Guetlein
> wrote:
>>
>> Martin
>>
>>
>>
>> One more thing, how can I adjust the color of the label?
>> Example:
>> draw ID bb2 BOUNDBOX color whit
Hi,
What is the best way to render a compound as a sphere (a single c-atom)?
I am displaying a cloud of compounds at once, and I would need to
switch easily between the normal compound rendering, and the single
atom rendering. The view (3d-positions, zooming) should not change,
and the single sph
e moveto command:
>
> moveto 0.0 {0 0 1 0} 100.0 0.0 0.0 { 0 0 0 } 15.5
>
> Here indicating that 15.5 is the radius you want to be defined as
> full-screen at 100% (31 Angstroms across).
>
>
>
>
>
> On Fri, Mar 1, 2013 at 2:43 PM, Martin Guetlein <
> martin.guet
Hi,
I have a bit a strange issue:
When I load my dataset from a single file (a cloud of compounds) I can zoom
out easily until I have all the compounds on the screen.
When I load the same dataset, split into multiple files, but with equal
compounds in total and equal coordinates, I cannot zoom out
analysis%5C.googlecode%5C.com&l=967>
>>
>> On Mon, Feb 11, 2013 at 12:10 PM, Robert Hanson wrote:
>>
>>> The closest I could suggest would be using the dimensions of a boundBox.
>>> You are right that there is significant math if you want "the tightest
>
Hi,
is there a convenient way to draw an ellipsoid that envelops a model?
This command would draw a sphere that envelops a model:
> ellipsoid ID AXES { 0 0} {0 0}
{0 0 } CENTER
But most compounds are sort of longish, and it would be nice to use an
ellipsoid for that (I fear that there is a lot
I added it to the "Applications using Jmol" list.
Thanks,
Martin
On Thu, Mar 29, 2012 at 5:44 PM, Angel Herráez wrote:
> Congratulations, Martin
>
> Have you added its URL and description to the Jmol wiki?
> "Websites using Jmol"
>
> :-)
>
>
> ---
Hi all,
I just wanted to let you now that we recently published our Jmol-based
viewer for small chemical compound datasets: http://ches-mapper.org
A big thanks to all people involved in Jmol.
Best regards,
Martin Gütlein
--
Dipl-Inf. Martin Gütlein
Phone:
+49 (0)761 203 7633 (office)
+49 (0)177
Hi,
-- Forwarded message --
From: Robert Hanson
Date: Mon, Sep 19, 2011 at 5:16 PM
Subject: Re: [Jmol-users] problem when selecting smarts [#6]-[#6]
To: jmol-users@lists.sourceforge.net
>
> That's fixed at http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
> I've also m
Mon, Sep 19, 2011 at 7:18 AM, Robert Hanson wrote:
>>
>> Ah! I see. Right. This is a specific problem to [#n] because those cases
>> are ambiguous in relation to aromaticity. I'm on to it. Thanks.
>>
>>
>> On Mon, Sep 19, 2011 at 2:46 AM, Martin Guetlein
&g
s the smarts fragments:
[#6]-[#6]
http://opentox.informatik.uni-freiburg.de/depict?data=[H]C%3D1C%28[H]%29%3DC%28[H]%29C%28%3DC%28C%3D1%28[H]%29%29C%28F%29%28F%29F%29S[H]&smarts=[%236]-[%236]
Best regards,
Martin
>
> On Sun, Sep 18, 2011 at 4:46 PM, Martin Guetlein
>
1([H]))C(F)(F)F)S[H]
$ select smarts("[#6]-[#6]")
7 atoms selected
Best regards,
Martin
>
>
>
> On Fri, Sep 16, 2011 at 6:25 AM, Martin Guetlein <
> martin.guetl...@googlemail.com> wrote:
>
>> Hi,
>>
>> I would like to match the following sm
Hi,
One more smarts matching issue.
[#6][#7] should match both compounds:
[H]C1=C([H])C(=C([H])C(=C1([H]))S[H])[N+](=O)[O-]
(depicted:
http://www.daylight.com/daycgi/depict?5b485d43313d43285b485d2943283d43285b485d2943283d4331285b485d2929535b485d295b4e2b5d283d4f295b4f2d5d
)
[H]C1=C([H])C(=C([H])
Hi,
I would like to match the following smarts [#6]-[#6], which is two carbon
atoms connect with single bond.
The problem: 'select smarts("[#6]-[#6]")' seems to ignore the bond type and
selects all pairs of carbons, even those who are aromatic.
It is not an aromticity detection problem, as 'sele
Hi,
is it possible to determine if a 2d point (mouse click) is inside/outside a
boundinx box?
I had a look at modelset.BoxInfo, but could not find it. There is a
isWithin()-method for 3d points, but not for the 2d - mapping of the box.
Cheers,
Martin
--
Dipl-Inf. Martin Gütlein
Phone:
+49 (0)
On Thu, Sep 8, 2011 at 5:48 PM, Martin Guetlein <
martin.guetl...@googlemail.com> wrote:
>
>
> On Thu, Sep 8, 2011 at 5:43 PM, Robert Hanson wrote:
>
>> Oh, I lied. Just use
>>
>> boundbox [some definition here]
>> draw ID bb1 BOUNDBOX mesh nofill
works, thanks
Martin
>
>
> On Thu, Sep 8, 2011 at 10:30 AM, Martin Guetlein <
> martin.guetl...@googlemail.com> wrote:
>
>>
>>
>> On Thu, Sep 8, 2011 at 5:14 PM, Robert Hanson wrote:
>>
>>> Only by hand -- using DRAW commands.
>>>
On Thu, Sep 8, 2011 at 5:14 PM, Robert Hanson wrote:
> Only by hand -- using DRAW commands.
>
How can I give objectids to the boundingbox (sth like 'draw boundbox2').
Could you give an example?
Thanks,
Martin
>
> On Thu, Sep 8, 2011 at 10:12 AM, Martin Gue
Hi,
can I somehow draw more than one boundbox?
Best regards,
Martin
--
Dipl-Inf. Martin Gütlein
Phone:
+49 (0)761 203 7633 (office)
+49 (0)177 623 9499 (mobile)
Email:
guetl...@informatik.uni-freiburg.de
--
Doing More w
Hi Angel,
thanks for the hint, I just retried, and found out that I have to load the
dataset first, then call "hover off" (its _not_ working the other way
around).
Martin
2011/9/2 Angel Herráez
> Hi Martin
> "hover off"
> is what makes it. It works for me (12.2.RC5, single model loaded)
>
>
>
Hi all,
I have one more issue. How can I disable that label that appears when
hovering the mouse over an atom (text is atom info, sth. like 'C12/2.1 #12')
?
Things I tried that did not work:
hover OFF
label OFF
set drawHover OFF
set labelAtom OFF
set hoverLabel ''
Thanks for helping,
Viele Grüß
Thanks a lot
Martin
On Tue, Aug 30, 2011 at 11:18 PM, Robert Hanson wrote:
> sure -- just added
>
> set minPixelSelRadius (default 6)
>
> On Tue, Aug 30, 2011 at 7:21 AM, Martin Guetlein <
> martin.guetl...@googlemail.com> wrote:
>
>> Hello all,
>>
&
Hello all,
I am using jmol in as part of my java application. I would like the
findNearestAtomIndex(x,y) function to be less strict. I.e. you really have
to be Johnny on the spot when clicking a compound that is farther away.
I checked the source code and found the critical spot: The class
AtomCol
Hello Jmol-Users,
I'm new to Jmol, and I would like to translate single molecules
instead of the whole set.
The following example script:
model 1
// select molecule=1 // does not make a difference
translateSelected {30 0 0}
model 1 - 2
.. translates molecules 1 and 2 (i.e.both molecules end up a
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