Interesting use case!
Egon
http://enanomapper.net/
On Fri, Jun 20, 2014 at 8:37 AM, Kazem Sepehrinia ksepehri...@gmail.com wrote:
Hi,
I have made a silica nanoparticle using Materials Studio and I want to
modify surface chemistry of it, I want to remove unwanted groups from the
surface and
Bob,
On Fri, Jun 20, 2014 at 9:31 AM, Angel Herráez angel.herr...@uah.es wrote:
I do not think that Jmol is your best tool for that, since I am
guessing there will be a lot of (repetitive) silica groups to which
the new groups must be added. Removal of groups is probably easy.
For just one
Kazem,
On Fri, Jun 20, 2014 at 8:37 AM, Kazem Sepehrinia ksepehri...@gmail.com wrote:
I have made a silica nanoparticle using Materials Studio and I want to
modify surface chemistry of it, I want to remove unwanted groups from the
surface and create some new groups on the surface of
On Fri, Jun 20, 2014 at 12:46 PM, Angel Herráez angel.herr...@uah.es wrote:
My concerns are about correct atom position, and also adding more
atoms that were not present and should go in the right positions too.
Understood and agreed... if I think of the nanotox field, however,
they typically
Hi all,
the CDK has code to read CML files with a JMOL-ANIMATION convention
which was one used to store Jmol animations in the Chemical Markup
Language.
Is anyone using this convention or using CML in general for conventions?
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
On Thu, Mar 6, 2014 at 3:49 PM, Robert Hanson hans...@stolaf.edu wrote:
What does that even mean, Jmol-Animation convention?
convention is a concept from the Chemical Markup Language format. A
convention refers to how various CML elements encode particular
content.
And how could you possibly
On Thu, Mar 6, 2014 at 4:00 PM, Robert Hanson hans...@stolaf.edu wrote:
sure. I see. Right. Standard, simple animation. Thank you.
And your questions basically confirm my suspicion :)
Thanks,
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University
On Wed, Apr 3, 2013 at 10:33 PM, Robert Hanson hans...@stolaf.edu wrote:
Oh my! http://www.chm.bris.ac.uk/jmol/jmol-7/
Nice, but it does not beat Jmol 0.6 from March 2001:
jmol-0.6.1.tar.gz 2001-03-26 2.9 MB
- https://sourceforge.net/projects/jmol/files/OldFiles/
That said, there is not much
On Fri, Feb 22, 2013 at 5:59 PM, Robert Hanson hans...@stolaf.edu wrote:
A lofty goal. No such plans at this stage.
Understood, and no worries :) There will always be plenty of ideas,
but without the bank account of someone like Gates or Slim, we won't
be able to implement them all :)
Plenty
On Fri, Feb 22, 2013 at 1:27 AM, Robert Hanson hans...@stolaf.edu wrote:
Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is still
work to be done to ensure faithful rendition, but it's a start.
Nice!
Do you also have in mind of writing such files? That would very nicely
On Wed, May 16, 2012 at 11:00 PM, Robert Hanson hans...@stolaf.edu wrote:
Thank you, Nico, for releasing Jmol 12.3.25. This version of Jmol is very
special. It includes
set forcefield MMFF
Well done!
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
On Sun, Apr 22, 2012 at 10:40 PM, Eric Martz ema...@microbio.umass.edu wrote:
This is the first I've heard about PWF. There are some slides by
Helen Berman about it here:
http://www.rcsb.org/pdb/general_information/about_pdb/rcsbpdbac10-presentations.pdf
Listening to a talk from Gerard
On Fri, Apr 13, 2012 at 7:03 AM, Robert Hanson hans...@stolaf.edu wrote:
OK. Please test!
http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
Very nice!
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University
Hi Jonathan,
On Fri, Mar 23, 2012 at 11:46 PM, Jonathan Gutow gu...@uwosh.edu wrote:
This suggests that there is a workaround for getting Jmol to work with the
IcedTea plugin. I thought from reading it that IcedTea couldn't handle the
segmented loading.
The applet loads for me nowadays in
On Thu, Mar 29, 2012 at 3:08 PM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote:
1. Do you want a QA controlled (by Apple) environment, or the more
advertising-oriented environment of Android?
I do have several Android apps installed without advertisement... I do
not think the above choice is
Dear Henry,
On Fri, Mar 30, 2012 at 11:01 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote:
I find it very disturbing that educators are even considering creating
a learning environment where students are restricted in their
learning! That is just another step back to the middle ages... Henry,
All,
On Fri, Mar 30, 2012 at 10:29 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
I find it very disturbing that educators are even considering creating
a learning environment where students are restricted in their
learning! That is just another step back to the middle ages... Henry
On Thu, Mar 29, 2012 at 4:19 AM, Craig T Martin cmar...@chem.umass.edu wrote:
I don't yet have an iPad personally, but it's on my list of things to buy
next and I have a number of colleagues who are absolutely fanatical.
Tomorrow we go to the Dean to pitch an idea that will involve the purchase
On Fri, Mar 23, 2012 at 8:33 PM, Eric Martz ema...@microbio.umass.edu wrote:
I just heard a segment on NPR about hundreds of high schools that are
abandoning textbooks and giving every student an iPad instead.
This is so sad... we're not even over the MS vendor lock-in, and ready
to buy into
2012/1/29 Herráez Sánchez Ángel angel.herr...@uah.es:
Everything you describe sounds like the regular and proper way to do. It may
be your browser, but I would not expect it.
Any modern browsers now behave, and Iceweasel is Gecko-based, right?
Iceweasel is just Firefox, but the name 'firefox'
2012/1/29 Herráez Sánchez Ángel angel.herr...@uah.es:
I recollect other people reporting problems with IcedTea, may be that.
...
jmolInitialize(.., JmolApplet.jar)
Yeah, I'd found that too and using the signed full jar... and that
works in Konqueror, Icedweasel, and Chrome.
So, I think we
cc:jmol-user
Hi Peter,
2012/1/16 Peter Sahlin peter.sah...@akademi.bastad.se:
Hope you can read my swedish, otherwise tell me and I will translate.
Yeah, I could read it :) I'm not a native speaker, but in the past
three years up picked it up a bit.
Hämtade Jmol 12.3.12 igår, men där fick
On Mon, Dec 5, 2011 at 2:49 PM, Robert Hanson hans...@stolaf.edu wrote:
https://market.android.com/search?q=jmolso=1
Cool! And now that I actually have an android, even cooler!
Q: is it possible to create a URL or so, that would auto load the app
with a particular protein? Or better: with a
://lists.sourceforge.net/lists/listinfo/jmol-users
Scroll down the bottom, enter your subscribed email address and click
the Unsubscribe button.
With kind regards,
Egon Willighagen
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm
On Tue, Nov 22, 2011 at 3:41 AM, Robert Hanson hans...@stolaf.edu wrote:
We just discovered that Jmol PNG images inserted in Google Documents
preserve their state after saving as zipped HTML.
What state are you referring to here? Does Jmol include a script to
restore the view as metadata in the
On Fri, Oct 14, 2011 at 1:02 AM, Robert Hanson hans...@stolaf.edu wrote:
http://chemapps.stolaf.edu/jmol/docs/examples-12/isomers.htm
What's up with example 4? The MFs don't match... or is that intentional?
Just thought of this idea -- will be developing the page to have more
examples. Note
On Mon, Sep 19, 2011 at 9:46 AM, Martin Guetlein
martin.guetl...@googlemail.com wrote:
I think the aromatic bonds not should be matched.
I think the '~' bond should match any bond and ':' aromatic bonds, but
'-' is explicit for single bonds...
Egon
--
Dr E.L. Willighagen
Postdoctoral
Hi MediaWiki-plugin users,
while something like jmolSmilesCC/jmolSmiles works fine, when I
try to use this in a Template environment, like with:
jmolSmiles text=3D (Jmol){{{Has Smiles|}}}/jmolSmiles
it does not work... the {{{Has Smiles|}}} is properly set, but the
applet gets not the SMILES
On Wed, Sep 14, 2011 at 10:09 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
jmolSmiles text=3D (Jmol){{{Has Smiles|}}}/jmolSmiles
I think a similar thing is happening with
jmolFile{{{CMLFile|}}}/jmolFile which now gives me this exception:
Catchable fatal error: Argument 1 passed
On Wed, Sep 14, 2011 at 7:05 AM, Brian Salter-Duke
b_d...@bigpond.net.au wrote:
On Wed, Sep 14, 2011 at 12:44:11AM +0200, Angel Herr?ez wrote:
https://wiki.ch.ic.ac.uk/wiki/index.php?title=User_talk:Rzepa1
All applets in there work for me:
That's in Fiirefox 6.0.2, WinXP, Java 1.6.0_27
Hi all,
On Sun, Jul 31, 2011 at 2:12 AM, Robert Hanson hans...@stolaf.edu wrote:
On Sat, Jul 30, 2011 at 3:42 PM, Richard Ball r...@ellerbach.com wrote:
Egon, what do you recommend?
R,S stereochemistry is a very complex algorithm. I have a limited
implementation in the CDK of the published
On Sun, Jul 31, 2011 at 10:54 PM, Richard Ball r...@ellerbach.com wrote:
Thanks Mike. The problem I want to provide a solution for (assuming there is
one) is: if someone has/gets a .mol file with a complex multi-stereocenter
molecule how can they get the R/S assignment for the particular atoms
Hi Eric,
On Sat, Jun 18, 2011 at 11:59 PM, Eric Martz ema...@microbio.umass.edu wrote:
Does anyone know of an animation simulation (atomic coordinates) for
changes in 3D protein conformation (or amino acid conformation) due
to changes in pH?
I took the liberty to cross-post your question on
On Thu, May 19, 2011 at 3:45 PM, Robert Hanson hans...@stolaf.edu wrote:
I've done a bit of work on my demo page for viewing molecular orbitals and
turned it into the Jmol Molecular Orbital Viewer.
See http://stolaf.edu/people/hansonr/jmol/mo
Filled is green, empty is red?
Egon
--
Dr E.L.
On Tue, Apr 12, 2011 at 4:32 PM, Robert Hanson hans...@stolaf.edu wrote:
irc://chat.freenode.net:8001/wikichem to start at 1500 UTC. Feel free to
join us. Options for Jmol in Wikipedia.
Did you try:
http://webchat.freenode.net/
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet
On Thu, Apr 7, 2011 at 1:51 PM, Robert Hanson hans...@stolaf.edu wrote:
Otis Rothenberger and I have been working on ways to improve the
accessibility of Jmol to novice users, and I think we have something. Please
check this out:
http://chemapps.stolaf.edu/jmol/jmol.php
Nice!
Egon
--
Dr
Bob,
nice!
On Wed, Feb 9, 2011 at 6:43 PM, Shore, Jay jay.sh...@sdstate.edu wrote:
I like it a lot – thank you for developing it.
Interestingly, on my MacBook (10.6.6) the slider works with Firefox (4.0b1)
but not with Safari (5.0.3) nor Chrome (9.0.597.94 beta).
Firefox (as IceWeasel)
2011/1/18 Angel Herráez angel.herr...@uah.es:
Just my 2 cents:
Evidently, a fair number of PubChem's sdf's have partial charge data.
I see aproblem here. The format shown in your example is not
according to SDF spec (I think it does not suppor partial charge,
only formal charge).
How so?
On Fri, Jan 14, 2011 at 11:42 AM, philippe philippe.maill...@wanadoo.fr wrote:
pouvez vous m'indiquer la procédure pour installer Jmol sous ubuntu pour
visualiser des molécules
You just download the Jmol.jar and start it from the command line with Java:
$ sudo aptitude install openjdk-6-jre
On Fri, Jan 14, 2011 at 1:32 PM, philippe philippe.maill...@wanadoo.fr wrote:
Just a last question, I may open an plug-in chime with Jmol.
Jmol has a scripting language quite similar to that of Chime, but
which has evolved enormously since the Chime days... is that what you
mean?
Documentation
Hi Nico,
On Wed, Nov 24, 2010 at 9:39 PM, Nicolas Vervelle nverve...@gmail.com wrote:
A French medical TV show has just used a picture of THC rendered with Jmol
for a few seconds.
Not much, but that's still nice to know.
The broadcast is available for a few days
at
On Sun, Nov 28, 2010 at 11:26 AM, Nicolas Vervelle nverve...@gmail.com wrote:
The link works, but the video does not :( I get on hold for 35
seconds, and then only get a white video canvas :(
It's working for me : 35 seconds of ads, then video canvas where I click on
play (I had to click
2010/11/4 Jan Halborg Jensen jhjen...@kemi.ku.dk:
has anyone succeeded in embeding an interactive Jmol model in a google site
web site?
I just asked the other day about using it on blogger.com (=Google) hosted blogs:
On Fri, Oct 22, 2010 at 12:16 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote:
http://www.theregister.co.uk/2010/10/21/apple_threatens_to_kill_java_on_the_mac/
As of the release of Java for Mac OS X 10.6 Update 3, the version of Java
that is ported by Apple, and that ships with Mac OS X, is
On Fri, Oct 22, 2010 at 12:33 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote:
http://lists.apple.com/archives/Java-dev/2010/Oct/msg00248.html
That expresses future aspirations, rather than testable reality. There is
nothing for
OS X at http://openjdk.java.net/
You can find instructions
On Thu, Oct 21, 2010 at 3:17 PM, Philip Bays pb...@saintmarys.edu wrote:
Anyone apply the Java update released yesterday? If so, did it break
anything?
Somewhat related, but also somewhat OT... have people been using
OpenJDK on OS/X? Is that possible yet, as it seems Java will phase out
their
On Wed, Sep 1, 2010 at 11:05 PM, Robert Hanson hans...@stolaf.edu wrote:
done. I retro-added it to 12.0, just because.
Jmol 12.1.9 and 12.0.11 will have sp3d and sp3d2 hybridizations. See
documentation for details.
Yeah, I saw it in the changelog yesterday! Cool!
I will blog about this
On Thu, Sep 2, 2010 at 9:21 PM, Robert Hanson hans...@stolaf.edu wrote:
This just in!
Congrats!
Egon
--
Dr E.L. Willighagen
Post-doc @ Uppsala University (only until 2010-09-30)
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
LinkedIn:
On Fri, Aug 20, 2010 at 5:53 AM, Robert Hanson hans...@stolaf.edu wrote:
Thank you, Paul, for contacting us about this error. Looks like we had a bug
that only appears for first-time users.
Ah, so it was a folder that did not exist?
Egon
--
Dr E.L. Willighagen
Post-doc @ Uppsala University
Hi Paul,
On Fri, Aug 13, 2010 at 3:01 PM, Paul A Craig pac8...@rit.edu wrote:
I am trying to run Jmol on my LInux 9.10 computer and keep getting this error
message. I am new to Linux and am not a java programmer. I see the same
problem on my Mac.
I am running Ubuntu 10.04 with Java
On Wed, Aug 11, 2010 at 6:08 PM, Philip Bays pb...@saintmarys.edu wrote:
I just got this response from the author of the Java Embedding Plugin that
the Mozilla browsers use to implement Java applets on the Mac. A solution
may be in sight:=)
Great! Thanx for getting in contact with them!
Egon
Hi all,
I saw some interesting emails lately on the scripts and sorts... has
anyone yet considered using MyExperiment.org for sharing useful Jmol
scripts?
Would that be an interesting platform to share Jmol scripts like:
Show the heme groups in protein X.
Demonstrate the hydrogen bonding
On Wed, Jul 28, 2010 at 4:10 PM, Robert Hanson hans...@stolaf.edu wrote:
Here's a listing of all the new capabilities of Jmol 12.0, categorized:
http://chemapps.stolaf.edu/jmol/docs/examples-12/new12.htm
Congrats, Bob!
Egon
--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse
On Tue, Jul 27, 2010 at 1:58 PM, Robert Hanson hans...@stolaf.edu wrote:
we just need to have someone with a Mac use their Java Preferences App to
set the preference for applets to Java 1.5 and see if it fixes the problem.
I think it will. If so, then clearly it IS a Java 1.6 issue.
I would
On Thu, Jul 15, 2010 at 2:59 PM, Van der Lee avder...@univ-montp2.fr wrote:
Bob's fix worked well (thanks!):
http://www.dicoscouts.x10hosting.com/perez.pdf
Can anyone suggest a reader for Linux that supports this live content?
I tried Okular [0], but that showed an empty slide :(
Egon
On Thu, Jul 15, 2010 at 5:04 AM, Robert Hanson hans...@stolaf.edu wrote:
Can someone explain to me how the combination of HTML5 and WebGL is a
replacement for Java?
It is not so much the Java language as it is the Applet design... the
applet concept requires a plugin to be installed (with the
See:
http://blueobelisk.shapado.com/questions/should-i-use-jmol-or-chemdoodle-for-developing-a-3d-application
Eg.
--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList:
On Fri, May 28, 2010 at 7:52 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
On May 28, 2010, at 10:22 AM, Robert Hanson wrote:
This uses a web service at Indiana University
http://cheminfo.wikispaces.com/smi23d
that appears to use PCMODEL for its converter. The idea is similar
to the
On Fri, May 28, 2010 at 4:30 AM, Robert Hanson hans...@stolaf.edu wrote:
137. set picking dragMinimizeMolecule -- responsive docking
With Jmol 12.0.RC15 you can move a small molecule around and watch it react
to its environment. Grab the caffeine molecule and move it toward the
protein.
Hi Bob,
On Thu, May 13, 2010 at 5:12 AM, Robert Hanson hans...@stolaf.edu wrote:
Probably what we should do is write a simple open-source version of JME to
provide a frame to JmolSmilesApplet. It's too bad that Peter's work is not
extensible in that regard. Peter, you sure you don't want to do
Hi Bob,
I'm impresses, once more... and don't want to spoil the news of this
powerful API! But...
On Wed, May 5, 2010 at 8:07 PM, Robert Hanson hans...@stolaf.edu wrote:
select smarts(C(F)[...@](Cl)H)
... this molecule is not chiral...
How does your lib handle the SMILES listed by Noel:
On Wed, May 5, 2010 at 8:17 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Wed, May 5, 2010 at 8:07 PM, Robert Hanson hans...@stolaf.edu wrote:
select smarts(C(F)[...@](Cl)H)
... this molecule is not chiral...
But then again, it's a SMARTS, not SMILES... so, it's fine
On Wed, May 5, 2010 at 9:03 PM, Robert Hanson hans...@stolaf.edu wrote:
those should all be fine. They are similar to all the ones I tested. It's a
full range of [...@1] [...@th2] [C@@] [...@h] etc. The parser accepts the
defaults for two-, four-, five-, and six-bond situations (AL, TH, TP,
On Thu, May 6, 2010 at 4:34 AM, Robert Hanson hans...@stolaf.edu wrote:
What the heck! Might as well do them all!
So, can these chiral SMILES also be used to create a 3D model? Where
the stereo is correctly applied?
Egon
--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of
On Wed, Apr 28, 2010 at 3:59 PM, Robert Hanson hans...@stolaf.edu wrote:
I propose that Jmol 12.0 officially require Java 1.5. This will allow easy
expansion of several features, including parallel processing, which we just
introduced for isosurface creation.
Java5 is out of service too, and
Nice blog post with a small request (please leave as comment in blog too):
http://sea36.blogspot.com/2010/04/creating-pngs-from-jmol.html
I think Sam's question is about the following: is it possible with the
Jmol.js to show a (pre-compiled?) PNG image of a structure which can
be clicked to open
On Wed, Apr 21, 2010 at 8:42 PM, Robert Hanson hans...@stolaf.edu wrote:
I know I'm not the first to think of doing this -- what else is out there in
this regard?
There used to be a script to convert a Chime script into a Jmol
script... have you used that?
Egon
--
Post-doc @ Uppsala
On Fri, Apr 9, 2010 at 11:29 PM, Jonathan Gutow gu...@uwosh.edu wrote:
J. Chem. Ed. has just published a brief description of Jmol and the
export to web function as well as archived a copy of the tutorial I
put together. I'll add the link to the Wiki, but post it here in case
anybody cares.
Bob,
On Wed, Apr 7, 2010 at 5:37 PM, Robert Hanson hans...@stolaf.edu wrote:
I'm sure there is. And if VMD is any example, the use of GPUs would vastly
increase performance. It would be a great project for someone to explore.
Since I know nothing about parallel processing, I'm not the one to
Hi Hilmar,
Bob is the current code wizard... my Jmol code is long past history,
but we are using it in Jmol, and that needs an overhaul anyway... I
have been GSoC mentor in the past already, but could be available for
co-mentoring...
Bob, do you fancy a Google SoC T-shirt?
Egon
On Fri, Mar 26,
On Thu, Mar 25, 2010 at 2:58 PM, Robert Hanson hans...@stolaf.edu wrote:
This is fixed, and we will get a release out this weekend I hope.
Bob++
Egon
--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
Blog:
Hi Christian,
On Fri, Mar 26, 2010 at 1:32 AM, Christian M Zmasek czma...@burnham.org wrote:
I am the main developer of the Archaeopteryx phylogenetic tree viewer
(http://www.phylosoft.org/archaeopteryx/).
For this year's Google Summer of Code (http://code.google.com/soc/) we
developed a
On Mon, Mar 8, 2010 at 2:57 PM, Robert Hanson hans...@stolaf.edu wrote:
That's ridiculous. Sorry, but to try to go retro on this is just too strange.
:)
I agree; don't shoot the messenger.
Egon
--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Hi all,
I saw this interesting question on the CCL mailing list:
On Tue, Mar 2, 2010 at 9:55 PM, Anthony F wrote:
My next question is on visualizing my XYZ files. I have used Avogadro, VMD,
and Gabedit. But I want to make diagrams like these:
Hi all,
our wiki has sections for Jmol-in-publications (getting overcrowded
:), Jmol-in-wiki's, etc... Just got this (old) link with Jmol (via
Bioclipse) in the movies :)
http://divby0.blogspot.com/2008/10/eclipse-photoshop-challenge-better-than.html
Happy new year all!
Egon
--
Post-doc @
Nina,
On Sun, Dec 27, 2009 at 11:55 AM, Nina Jeliazkova n...@acad.bg wrote:
I am looking for a guide or examples to use JMol in headless mode, for
generating images on the server side.
check out the answer on the Blue Obelisk Exchange:
On Fri, Dec 25, 2009 at 5:01 PM, Robert Hanson hans...@stolaf.edu wrote:
Did I forget to send this?
This video demonstrates a first go at incorporating multi-touch capability
into Jmol.
http://www.youtube.com/watch?v=7x8uDRQKIg0
I had not seen it yet. Nice video! Cool hardware...
Some time
On Wed, Dec 16, 2009 at 9:22 PM, Robert Hanson hans...@stolaf.edu wrote:
But I agree, the business with axes and tics and such is pretty far afield
of the core Jmol mission.
Not sure if ticks are must used in crystallography, but axes most
certainly... I also use the axes visualization in some
On Fri, Nov 20, 2009 at 5:08 PM, Robert Hanson hans...@stolaf.edu wrote:
Jmol is GPLP
That would be LGPL :)
Egon
--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
On Wed, Nov 18, 2009 at 10:38 PM, Jeff Hansen jhan...@depauw.edu wrote:
Lets just go extreme with this. Make every side of the applet available for
adjusting something. I could see zoom, Z-rotation, slab, atom size. Why
not just make it configurable so a little javascript or Jmol script can
On Thu, Nov 19, 2009 at 12:14 AM, Robert Hanson hans...@stolaf.edu wrote:
Why not just make it anywhere you want? any function?
Say, on top/around of a certain atom, bond or secondairy structure?
Egon
--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog:
On Thu, Nov 19, 2009 at 12:27 AM, Robert Hanson hans...@stolaf.edu wrote:
Hmm, I was thinking more along the lines of within a certain area of the
window. You can always trap a pickCallback for atoms.
True. I did not think of it that this could be done on a purely Jmol
script level too... how
Nice!
On Thu, Nov 19, 2009 at 12:43 AM, Robert Hanson hans...@stolaf.edu wrote:
function testit {
print _atomPicked
}
set pickCallback jmolscript:testit;
Egon
--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList:
Thanx, Henry!
http://www.nature.com/nchem/journal/v1/n7/media/nchem.373_jmol.html
Egon
--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
Hi all,
is Jmol still able to save the content? For example as CML or perhaps
MDL molfile or XYZ?
Egon
--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
On Fri, Oct 30, 2009 at 3:03 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote:
As it happens, Bob and I have been having a discussion about eg saving XYZ
(with
vibrational vectors). Bob's documentation does describe the process,
although of course
one has to use the signed applet to use the
On Wed, Sep 2, 2009 at 8:11 PM, N David Brownhubd...@googlemail.com wrote:
Given the 677 compounds tested and the proximity to the TSAR values, I
think that's an odd comment. It's an approximation, true, but for the
drop in computational cost I find the accuracy astounding.
So, just out of
On Sun, Aug 2, 2009 at 9:06 AM, Robert Hansonhans...@stolaf.edu wrote:
Can someone help here?
I think he registered after my reply.
Egon
--
Post-doc @ Uppsala University
http://chem-bla-ics.blogspot.com/
--
Let
Hi Bob!
On Sat, Aug 1, 2009 at 7:46 AM, Robert Hansonhans...@stolaf.edu wrote:
The 2009 Gordon Research Conference on Visualization in Science and
Education is over. It was unbelievably cool. It's strict policy not to
discuss anything that was at that meeting, so please don't ask me to do
Hi all,
I just uploaded Release Candidate 3 for Jmol 11.8 with the following changes:
# code: more efficient VRML export
# new feature: set helixStep 1,2,3,... sets step for quaternion-based
analysis of structure -- see 1C4D
# bug fix: 1C4D has [FOR] -- not accepted
# bug fix: color
On Fri, Jul 3, 2009 at 10:14 AM, Egon
Willighagenegon.willigha...@gmail.com wrote:
Rich asks in his blog:
http://depth-first.com/articles/2009/07/02/dear-lazyweb-does-jmol-support-output-for-use-with-3d-glasses
Egon
--
Post-doc @ Uppsala University
http://chem-bla-ics.blogspot.com/
Hi all,
bug fix release 11.6.25 for the stable Jmol series has just been made
available on SourceForge with the following changes:
# bug fix: select model=1 does not work (since 11.6.RC17!)
# bug fix: dipole offsetside not working for molecular dipole (EVER!)
# bug fix: 2 pixels off in y for
Hi all,
a new Jmol prerelease has been uploaded to SourceForge, bringing these
changes as listed in the changelog:
# bug fix: select model=1 does not work (since 11.6.RC17!)
# new application: JmolData.jar
# This application completely disallows any display -- it is totally formless
# There are
Hi all,
not too long after the .44 release the changes are piling up again;
see below. Downloads from:
http://sourceforge.net/project/showfiles.php?group_id=23629package_id=142353release_id=693156
# bug fix: load trajectory XXX.cif not applying fractional coordinates.
# bug fix: load trajectory
On Mon, Jun 29, 2009 at 5:06 AM, Robert Hansonhans...@stolaf.edu wrote:
In case there is anyone in the London/Oxford/Lancaster areas or
Berlin/Frankfurt areas who would like to get together and talk about Jmol
(or let me give a presentation!), here is my itinerary for July/Aug:
July 22 -
On Wed, Jun 24, 2009 at 11:41 AM, Jan H. Jensenjhjen...@kemi.ku.dk wrote:
The GAMESS reader sounds very interesting, but I haven't been able to
find any documentation on the web?
Usually, Bob puts up demos of new features at:
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
But I do
Hi all,
with Nico on holiday, I got to honour to make a Jmol release again,
after a very long time of not doing releases :)
I'm pleased to announce the Jmol Prerelease 11.7.44 with the following
changes by the every amazingly productive Bob:
# bug fix: write FRAMES also for trajectories
# new
On Wed, Jun 3, 2009 at 10:20 PM, Robert Hanson hans...@stolaf.edu wrote:
see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
Check it out!
Nice !
Egon
--
Post-doc @ Uppsala University
http://chem-bla-ics.blogspot.com/
On Thu, Jun 4, 2009 at 9:52 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Wed, Jun 3, 2009 at 10:20 PM, Robert Hanson hans...@stolaf.edu wrote:
see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
Check it out!
Nice !
BTW, I get an unexpected exception in step 2 of 17
On Tue, Jun 2, 2009 at 1:15 AM, Brian Salter-Duke b_d...@bigpond.net.au wrote:
On quality, I think that is a different and general concern. We try to
not use poor quality images, so we would try to use only good quality
Jmol data files. I am happy that we restrict the type of jmol files to a
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