Re: [Jmol-users] How to introduce coordinate system

[Angel Herráez]

On 22 Jun 2011 at 22:11, Martin Hediger wrote:
> Wonderful, do you mind pointing me to where I can read about this?

http://jmol.sourceforge.net/jslibrary/#jmolApplet


> So instead of writing commands explicitly into the jmolApplet 
> constructor call, I can write the path to a Jmol script?
> Eg.
> jmolApplet(400, ../jmolScripts/jmolScriptToDisplayBox.js);

But is that a Jmol script file, or a javascript file?

The syntax for calling a script file is to use the "script" command:

jmolApplet(400, script ../jmolScripts/jmolScriptToDisplayBox.js );

or, to be safer with the filename,

jmolApplet(400, script "../jmolScripts/jmolScriptToDisplayBox.js" );




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Re: [Jmol-users] Electron density maps - dots

[Robert Hanson]

wow. that's a HECK of a lot of dots. That actually works?

On Wed, Jun 22, 2011 at 2:05 PM, Greeves, Nick wrote:

> Many thanks. I couldn't get the precise syntax you suggest to work but from
> Bob's examples (which I must have been subliminally aware of) but
> zap;isosurface phase scale 0.5 atomicOrbital 2 1 0 POINTS 10
> worked fine.
> Maybe it was the Zeff value that disagreed with my file which is the
> hydride ion.
> All the best
> Nick
> --
> 3D Organic Animations http://www.chemtube3d.com
> Tel: +44 (0)151-794-3506 (3500 secretary)
>
>
>
> On 22 Jun 2011, at 19:31, 
> wrote:
>
>  On 6/22/2011 2:23 PM, Greeves, Nick wrote:
>
> I use Jmol to display atomic and molecular orbitals and it works well.
>
> I would like to be able to render simple atomic orbitals 1s, 2s, 2p as
>
> electron density maps made up of dots.
>
> Is this currently possible and if so what sort of input file would
>
> work best?
>
>
> Something like this
>
> http://ursula.chem.yale.edu/~chem125/125/answ/a198/Image69.gif
>
>  but
>
> better. Taken from
>
> http://ursula.chem.yale.edu/~chem125/125/answ/a198/a198.html
>
> 
>
> Best regards
>
> Nick
>
> --
>
>
>
> You can do much better than what is on these pictures!  In the newest
> Jmol try for example: isosurface color yellow atomicOrbital 4 2 -2 4.0
> POINTS  5000;
>
> See Bob Hanson pages with the most recent examples for full explanation.
>
> PM
>
>
>
>
> --
> Simplify data backup and recovery for your virtual environment with
> vRanger.
> Installation's a snap, and flexible recovery options mean your data is
> safe,
> secure and there when you need it. Data protection magic?
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>
>


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phone: 507-786-3107


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Re: [Jmol-users] BIG addition to Jmol -- CONTACT command

[Robert Hanson]

OK! Thank you, Eric! Right, and we can do all sorts of interesting things --
measure area, measure volume, pick out and visualize whatever ones we want,
adjust the VDW radii to suit (for example, to emphasize specific groups).
Most importantly, we can do just exactly what you describe -- show the
interaction in this interesting way. I happen to think the CONNECT option is
sort of interesting, but I don't know if that will catch on. Primarily what
is cool, in my mind, is how accessible this is. You can even use it right
now at the Protein Data Bank. All you do is open up a Jmol structure viewing
page there and then add this to your URL:

  &JMOLJAR=
http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned.jar

For example:


http://www.rcsb.org/pdb/explore/jmol.do?structureId=3HZ3&bionumber=1&JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned.jar

Now, open a console and type something such as this into it:**

select not ligand
wireframe -0.1
color cpk
display within(group, within(5,ligand))
zoomto {ligand} 0
contact hbond {ligand}

or

contact hydrophobic {ligand}

or maybe

contact {ligand} parameters [0.5] NCI intermolecular

(We're still fine tuning those NCI parameters. Perhaps Julia can suggest
some adjustments there.  I can see already that we need a MINSET parameter
there, and I see I should adjust the "hydrophobic" because I see it is
picking up the ionic interactions as well.)

Most importantly, this is all SO accessible. There is absolutely no reason
NOT to check it out, and we think it produces very nice definitely
publication-quality graphics in a matter of minutes.

By the way, I'm still working on a good way to fine-tune the graphics. I'm
thinking that a mode that allows rapid setting and moving of labels (set
picking LABEL, followed by clicking for a label and SHIFT for moving them)
plus maybe a double-click? to undisplay a group --

  display displayed and not within(group, atomindex=_atomPicked)

We should think about what sets of commands would take care of this and get
them into the menu, maybe under "publication..."

Bob



On Wed, Jun 22, 2011 at 12:52 PM, Eric Martz wrote:

> Dear Bob,
>
> This is indeed very exciting!
> Kinemages and KiNG (by David and Jane Richardson)
> http://kinemage.biochem.duke.edu/
>
> use a similar display to show "bumps" or "clashes", namely volumes
> where the van der Waals radii of atoms overlap (and hence the atoms
> are impossibly close). This is one of the most powerful features of KiNG.
>
> The display is similar to your example "contact DENSITY 0.2 HBOND".
>
> The Richardson's MolProbity server is one of the most powerful (and
> unique) protein model quality assessment tools.
> http://molprobity.biochem.duke.edu/
>
> Among many other things, MolProbity first adds hydrogen atoms
> (enabling "all-atom contact analysis"), and then finds all clashes in
> a macromolecular model and constructs a kinemage (viewable in the
> java applet KiNG) to show them. It then calculates an overall
> clashscore, and compares this to the clashscores of other entries in
> the PDB with similar resolution. A bad clashscore means the model is iffy.
>
> It seems that Jmol is now close to doing a similar display. This
> would be fantastic!
>
> You can see a snapshot of their graphics for an hbond (green) and a
> bad clash (red) here:
> http://www.umass.edu/molvis/tmp/king-snaps/hbond-clash.png
>
> The hbond is between a hydrogen and a main-chain oxygen. The clash is
> between two hydrogens. They color "bad overlaps" red.
>
> They also show small overlaps as yellow and orange:
> http://www.umass.edu/molvis/tmp/king-snaps/small-overlaps.png
>
> And vdW contacts as green/blue:
> http://www.umass.edu/molvis/tmp/king-snaps/vdw.png
>
> The rotatable KiNG with checkboxes for 1d66, from which the above
> snapshots were taken, is here
> (server is slow today, be patient)
>
>
> http://molprobity.biochem.duke.edu/viewking.php?MolProbSID=344oifg8bqtuhlpommroicf6e6i4mvtg&url=data/344oifg8bqtuhlpommroicf6e6i4mvtg/kinemages/1d66FH-multi.kin.gz
>
> or try this
> http://tinyurl.com/43bfzth
>
> Here is the clashscore page:
>
> http://molprobity.biochem.duke.edu/index.php?MolProbSID=344oifg8bqtuhlpommroicf6e6i4mvtg&eventID=87
> or
> http://tinyurl.com/3wm7hxg
>
> -Eric
>
> At 6/22/11, Robert Hanson wrote:
> >Jmol users --
> >
> >Not "big" as in lots of bytes, but BIG in terms of impact. I believe
> >Erik Wyatt (undergraduate at St. Olaf) and I have cracked the
> >nonbonding interations nut. With this announcement we hereby
> >introduce what I just checked in as Jmol 12.1.51_dev: the CONTACT
> >command. This new command displays objects that float in space
> >between two interacting atoms. These could be hydrophobic
> >interactions or hydrogen bonds or in principle any other
> >interactions. A set of "teasers" can be found at
> >
> http://stolaf.edu/people/hansonr/jmol/contact/2bxa.htm
> >
>  [snip]
>
>
>
> -

Re: [Jmol-users] How to introduce coordinate system

[Martin Hediger]

Wonderful, do you mind pointing me to where I can read about this?
So instead of writing commands explicitly into the jmolApplet 
constructor call, I can write the path to a Jmol script?
Eg.
jmolApplet(400, ../jmolScripts/jmolScriptToDisplayBox.js);
?








Am 22.06.11 20:50, schrieb Angel Herráez:
> Hell Martin
>
> Easy! The 2nd parameter in jmolApplet can take any commands, not just load.
> So,
>
>>   jmolApplet(400, "load 1PDB.pdb; axes on; boundbox on;");
>
>
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[Jmol-users] Electron density maps - dots

[Greeves, Nick]

Many thanks. I couldn't get the precise syntax you suggest to work but from 
Bob's examples (which I must have been subliminally aware of) but
zap;isosurface phase scale 0.5 atomicOrbital 2 1 0 POINTS 10
worked fine.
Maybe it was the Zeff value that disagreed with my file which is the hydride 
ion.
All the best
Nick
--
3D Organic Animations http://www.chemtube3d.com
Tel: +44 (0)151-794-3506 (3500 secretary)



On 22 Jun 2011, at 19:31, 
mailto:jmol-users-requ...@lists.sourceforge.net>>
 wrote:

 On 6/22/2011 2:23 PM, Greeves, Nick wrote:
I use Jmol to display atomic and molecular orbitals and it works well.
I would like to be able to render simple atomic orbitals 1s, 2s, 2p as
electron density maps made up of dots.
Is this currently possible and if so what sort of input file would
work best?

Something like this
http://ursula.chem.yale.edu/~chem125/125/answ/a198/Image69.gif
 but
better. Taken from
http://ursula.chem.yale.edu/~chem125/125/answ/a198/a198.html

Best regards
Nick
--


You can do much better than what is on these pictures!  In the newest
Jmol try for example: isosurface color yellow atomicOrbital 4 2 -2 4.0
POINTS  5000;

See Bob Hanson pages with the most recent examples for full explanation.

PM

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Re: [Jmol-users] linking a jmolCheckbox to a non-Jmol checkbox

[Angel Herráez]

Hello Yingjie 

Not sure what you mean exactly, but...

jmolCheckbox()  inserts a checkbox. You can include javascript commands as part 
of the JmolScript there, if you wish.

Alteratively, you write the source code for a checkbox and include a 
jmolScript(etc.) call in the 
onClick() or onChange() events



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Re: [Jmol-users] How to introduce coordinate system

[Angel Herráez]

Hell Martin

Easy! The 2nd parameter in jmolApplet can take any commands, not just load.
So,

>  jmolApplet(400, "load 1PDB.pdb; axes on; boundbox on;");



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Re: [Jmol-users] Electron density maps - dots

[Pshemak Maslak]

 On 6/22/2011 2:23 PM, Greeves, Nick wrote:
I use Jmol to display atomic and molecular orbitals and it works well. 
I would like to be able to render simple atomic orbitals 1s, 2s, 2p as 
electron density maps made up of dots.
Is this currently possible and if so what sort of input file would 
work best?


Something like this 
http://ursula.chem.yale.edu/~chem125/125/answ/a198/Image69.gif 
 but 
better. Taken from 
http://ursula.chem.yale.edu/~chem125/125/answ/a198/a198.html 


Best regards
Nick
--



You can do much better than what is on these pictures!  In the newest 
Jmol try for example: isosurface color yellow atomicOrbital 4 2 -2 4.0 
POINTS  5000;


See Bob Hanson pages with the most recent examples for full explanation.

PM
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[Jmol-users] Electron density maps - dots

[Greeves, Nick]

I use Jmol to display atomic and molecular orbitals and it works well. I would 
like to be able to render simple atomic orbitals 1s, 2s, 2p as electron density 
maps made up of dots.
Is this currently possible and if so what sort of input file would work best?

Something like this 
http://ursula.chem.yale.edu/~chem125/125/answ/a198/Image69.gif but better. 
Taken from http://ursula.chem.yale.edu/~chem125/125/answ/a198/a198.html
Best regards
Nick
--
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Director of Teaching and Learning
Department of Chemistry
University of Liverpool
Donnan and Robert Robinson Laboratories
Crown Street, LIVERPOOL L69 7ZD U.K.
Email address:ngree...@liverpool.ac.uk
WWW Pages:http://www.chemtube3d.com
Tel:+44 (0)151-794-3506 (3500 secretary)
Dept Fax:   +44 (0)151-794-3588







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Re: [Jmol-users] BIG addition to Jmol -- CONTACT command

[Eric Martz]

Dear Bob,

This is indeed very exciting!
Kinemages and KiNG (by David and Jane Richardson)
http://kinemage.biochem.duke.edu/

use a similar display to show "bumps" or "clashes", namely volumes 
where the van der Waals radii of atoms overlap (and hence the atoms 
are impossibly close). This is one of the most powerful features of KiNG.

The display is similar to your example "contact DENSITY 0.2 HBOND".

The Richardson's MolProbity server is one of the most powerful (and 
unique) protein model quality assessment tools.
http://molprobity.biochem.duke.edu/

Among many other things, MolProbity first adds hydrogen atoms 
(enabling "all-atom contact analysis"), and then finds all clashes in 
a macromolecular model and constructs a kinemage (viewable in the 
java applet KiNG) to show them. It then calculates an overall 
clashscore, and compares this to the clashscores of other entries in 
the PDB with similar resolution. A bad clashscore means the model is iffy.

It seems that Jmol is now close to doing a similar display. This 
would be fantastic!

You can see a snapshot of their graphics for an hbond (green) and a 
bad clash (red) here:
http://www.umass.edu/molvis/tmp/king-snaps/hbond-clash.png

The hbond is between a hydrogen and a main-chain oxygen. The clash is 
between two hydrogens. They color "bad overlaps" red.

They also show small overlaps as yellow and orange:
http://www.umass.edu/molvis/tmp/king-snaps/small-overlaps.png

And vdW contacts as green/blue:
http://www.umass.edu/molvis/tmp/king-snaps/vdw.png

The rotatable KiNG with checkboxes for 1d66, from which the above 
snapshots were taken, is here
(server is slow today, be patient)

http://molprobity.biochem.duke.edu/viewking.php?MolProbSID=344oifg8bqtuhlpommroicf6e6i4mvtg&url=data/344oifg8bqtuhlpommroicf6e6i4mvtg/kinemages/1d66FH-multi.kin.gz

or try this
http://tinyurl.com/43bfzth

Here is the clashscore page:
http://molprobity.biochem.duke.edu/index.php?MolProbSID=344oifg8bqtuhlpommroicf6e6i4mvtg&eventID=87
or
http://tinyurl.com/3wm7hxg

-Eric

At 6/22/11, Robert Hanson wrote:
>Jmol users --
>
>Not "big" as in lots of bytes, but BIG in terms of impact. I believe 
>Erik Wyatt (undergraduate at St. Olaf) and I have cracked the 
>nonbonding interations nut. With this announcement we hereby 
>introduce what I just checked in as Jmol 12.1.51_dev: the CONTACT 
>command. This new command displays objects that float in space 
>between two interacting atoms. These could be hydrophobic 
>interactions or hydrogen bonds or in principle any other 
>interactions. A set of "teasers" can be found at 
>http://stolaf.edu/people/hansonr/jmol/contact/2bxa.htm
> 
>
  [snip] 


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[Jmol-users] linking a jmolCheckbox to a non-Jmol checkbox

[Yingjie Lin]

Dear Jmol users,

Is there a way to link a jmolCheckbox to a non-Jmol checkbox? Just like what 
jmolSetCheckboxGroup can do to several jmolCheckboxes.

Thank you.

Yingjie Lin
Mount Sinai School of Medicine

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Re: [Jmol-users] MO HOMO/LUMO?

[Michael Evans]

Thanks, Bob. Can't fault WebMO for using the best 3D visualization software
on the web!

Cheers, Mike

On Wed, Jun 22, 2011 at 9:49 AM, Robert Hanson  wrote:

> OK, Mike. It was a simple bug fix. Jmol just wasn't processing the orbital
> occupancy data correctly.  See
> http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip  for the fix.
> I've also fixed that in Jmol 12.0, but that release will be later this week
> or next week, probably.
>
>
> ps: WebMO uses Jmol, by the way
>
>
> 2011/6/22 Michael Evans 
>
>> I just refreshed my Jmol version, to no avail. See attached for one
>> example of a file that doesn't work (although none work for me right now; at
>> least none that I've created with WebMO ).
>>
>> Cheers, Mike
>>
>> On Wed, Jun 22, 2011 at 1:37 AM, Robert Hanson wrote:
>>
>>> They won't work if your data does not have occupancy information. Please
>>> check the latest version, and/or send me the offending file so I can check
>>> it out.
>>>
>>> On Mon, Jun 20, 2011 at 5:53 PM, Michael Evans wrote:
>>>
 Lords & lasses of Jmol—in several versions of Jmol 12.0 (at least since
 .34), the "mo homo" and "mo lumo" commands don't seem to be working. The
 documentation seems to suggest they still should. Bug here? Could someone
 test this to see if I'm the only one having this issue?

 Cheers, Mike

 --
 Mike Evans
 Organic Chemistry Graduate Student
 Moore Group
 University of Illinois, Urbana-Champaign


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>>>
>>>
>>> --
>>> 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 what we want,
>>> it is better to take what answer we get.
>>>
>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>
>>>
>>> --
>>> Simplify data backup and recovery for your virtual environment with
>>> vRanger.
>>> Installation's a snap, and flexible recovery options mean your data is
>>> safe,
>>> secure and there when you need it. Data protection magic?
>>> Nope - It's vRanger. Get your free trial download today.
>>> http://p.sf.net/sfu/quest-sfdev2dev
>>>
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> Mike Evans
>> Organic Chemistry Graduate Student
>> Moore Group
>> University of Illinois, Urbana-Champaign
>>
>>
>> --
>> Simplify data backup and recovery for your virtual environment with
>> vRanger.
>> Installation's a snap, and flexible recovery options mean your data is
>> safe,
>> secure and there when you need it. Data protection magic?
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>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> 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 what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
> --
> Simplify data backup and recovery for your virtual environment with
> vRanger.
> Installation's a snap, and flexible recovery options mean your data is
> safe,
> secure and there when you need it. Data protection magic?
> Nope - It's vRanger. Get your free trial download today.
> http://p.sf.net/sfu/quest-sfdev2dev
> ___
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> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
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Moore Group
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Re: [Jmol-users] MO HOMO/LUMO?

[Robert Hanson]

OK, Mike. It was a simple bug fix. Jmol just wasn't processing the orbital
occupancy data correctly.  See
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip  for the fix.
I've also fixed that in Jmol 12.0, but that release will be later this week
or next week, probably.


ps: WebMO uses Jmol, by the way

2011/6/22 Michael Evans 

> I just refreshed my Jmol version, to no avail. See attached for one example
> of a file that doesn't work (although none work for me right now; at least
> none that I've created with WebMO ).
>
> Cheers, Mike
>
> On Wed, Jun 22, 2011 at 1:37 AM, Robert Hanson  wrote:
>
>> They won't work if your data does not have occupancy information. Please
>> check the latest version, and/or send me the offending file so I can check
>> it out.
>>
>> On Mon, Jun 20, 2011 at 5:53 PM, Michael Evans wrote:
>>
>>> Lords & lasses of Jmol—in several versions of Jmol 12.0 (at least since
>>> .34), the "mo homo" and "mo lumo" commands don't seem to be working. The
>>> documentation seems to suggest they still should. Bug here? Could someone
>>> test this to see if I'm the only one having this issue?
>>>
>>> Cheers, Mike
>>>
>>> --
>>> Mike Evans
>>> Organic Chemistry Graduate Student
>>> Moore Group
>>> University of Illinois, Urbana-Champaign
>>>
>>>
>>> --
>>> EditLive Enterprise is the world's most technically advanced content
>>> authoring tool. Experience the power of Track Changes, Inline Image
>>> Editing and ensure content is compliant with Accessibility Checking.
>>> http://p.sf.net/sfu/ephox-dev2dev
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> 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 what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>> --
>> Simplify data backup and recovery for your virtual environment with
>> vRanger.
>> Installation's a snap, and flexible recovery options mean your data is
>> safe,
>> secure and there when you need it. Data protection magic?
>> Nope - It's vRanger. Get your free trial download today.
>> http://p.sf.net/sfu/quest-sfdev2dev
>>
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Mike Evans
> Organic Chemistry Graduate Student
> Moore Group
> University of Illinois, Urbana-Champaign
>
>
> --
> Simplify data backup and recovery for your virtual environment with
> vRanger.
> Installation's a snap, and flexible recovery options mean your data is
> safe,
> secure and there when you need it. Data protection magic?
> Nope - It's vRanger. Get your free trial download today.
> http://p.sf.net/sfu/quest-sfdev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
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 what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Simplify data backup and recovery for your virtual environment with vRanger.
Installation's a snap, and flexible recovery options mean your data is safe,
secure and there when you need it. Data protection magic?
Nope - It's vRanger. Get your free trial download today.
http://p.sf.net/sfu/quest-sfdev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] MO HOMO/LUMO?

[Michael Evans]

I just refreshed my Jmol version, to no avail. See attached for one example
of a file that doesn't work (although none work for me right now; at least
none that I've created with WebMO ).

Cheers, Mike

On Wed, Jun 22, 2011 at 1:37 AM, Robert Hanson  wrote:

> They won't work if your data does not have occupancy information. Please
> check the latest version, and/or send me the offending file so I can check
> it out.
>
> On Mon, Jun 20, 2011 at 5:53 PM, Michael Evans wrote:
>
>> Lords & lasses of Jmol—in several versions of Jmol 12.0 (at least since
>> .34), the "mo homo" and "mo lumo" commands don't seem to be working. The
>> documentation seems to suggest they still should. Bug here? Could someone
>> test this to see if I'm the only one having this issue?
>>
>> Cheers, Mike
>>
>> --
>> Mike Evans
>> Organic Chemistry Graduate Student
>> Moore Group
>> University of Illinois, Urbana-Champaign
>>
>>
>> --
>> EditLive Enterprise is the world's most technically advanced content
>> authoring tool. Experience the power of Track Changes, Inline Image
>> Editing and ensure content is compliant with Accessibility Checking.
>> http://p.sf.net/sfu/ephox-dev2dev
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> 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 what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
> --
> Simplify data backup and recovery for your virtual environment with
> vRanger.
> Installation's a snap, and flexible recovery options mean your data is
> safe,
> secure and there when you need it. Data protection magic?
> Nope - It's vRanger. Get your free trial download today.
> http://p.sf.net/sfu/quest-sfdev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Mike Evans
Organic Chemistry Graduate Student
Moore Group
University of Illinois, Urbana-Champaign
[HEADER]
Version 2
Type UNIVERSAL
DefaultType MO 9
ValenceOnly TRUE
EnergyUnits HARTREE

[ATOMS]
16 0 0 0
8 2.76595970648207 0 0
8 -1.34698505019948 2.41578820520501 0

[BONDS]
2 1 2 
1 3 1 


[STO]
1 0 0 0 2 1.891185 1.10637709530662
1 1 0 0 1 1.658972 1.21151527895577
1 0 1 0 1 1.658972 1.21151527895577
1 0 0 1 1 1.658972 1.21151527895577
2 0 0 0 1 3.796544 9.14820421114255
2 1 0 0 0 2.389402 4.97904312820751
2 0 1 0 0 2.389402 4.97904312820751
2 0 0 1 0 2.389402 4.97904312820751
3 0 0 0 1 3.796544 9.14820421114255
3 1 0 0 0 2.389402 4.97904312820751
3 0 1 0 0 2.389402 4.97904312820751
3 0 0 1 0 2.389402 4.97904312820751

[MO1]
-37.551
2
1 -0.361967576912687
2 -0.0890108252180763
3 -0.151603468171057
4 3.8624187649307e-15
5 -0.545269376182472
6 0.104672166826941
7 -0.0204892755844904
8 4.69288221408105e-15
9 -0.545411736833502
10 -0.068877285567013
11 0.0814642789936161
12 4.37025864169186e-15

[MO2]
-36.377
2
1 -4.23605754252317e-05
2 -0.222943043886128
3 0.13092486727954
4 -2.519105258864e-16
5 -0.610218598127626
6 0.0866748033977096
7 0.0188140211946811
8 -2.41546024174744e-15
9 0.610087961115315
10 0.0257608384309185
11 -0.0848461095010319
12 2.87272865372802e-15

[MO3]
-21.328
2
1 0.656418032812003
2 0.0330542277414385
3 0.0562751620359262
4 6.62780291342127e-15
5 -0.426128023313266
6 -0.309163508338994
7 0.0135036161540141
8 -2.03190611637686e-15
9 -0.426132758076417
10 0.162358512764494
11 -0.26345585334676
12 -1.19912699670317e-15

[MO4]
-16.615
2
1 3.11844613731099e-06
2 -0.377557945325486
3 0.221739347222025
4 2.69877851691715e-15
5 0.306563436356196
6 0.476251306011742
7 0.204874492929655
8 7.2626507030314e-15
9 -0.30655266399534
10 0.0529511749981895
11 -0.515752372743619
12 -1.02310767457035e-15

[MO5]
-16.486
2
1 -5.30192201456712e-15
2 -2.81211311089519e-15
3 -5.31806269501814e-15
4 0.606781246750217
5 -5.14797679108437e-15
6 -1.0091523484021e-14
7 -6.70160076936926e-15
8 0.471849685792035
9 -2.3477057775327e-15
10 -5.13707495952309e-15
11 -3.34308944598126e-15
12 0.471870065506465

[MO6]
-15.823
2
1 -0.25876427572793
2 0.254724872963095
3 0.433712051420498
4 -2.10093006793064e-15
5 -0.0918453122265128
6 -0.0804187708077332
7 0.506797761376131
8 -3.83857449494761e-15
9 -0.0918716677754745
10 0.481832344757952
11 0.176527018491567
12 -2.54667837439549e-15

[MO7]
-12.638
2
1 1.50920357290703e-06
2 -0.0775801923659408
3 0.045556341151282
4 -1.63353772196577e-15
5 0.0465809668248679
6 0.226273193495166
7 -0.670749722004903
8 -2.38109394620711e-15
9

Re: [Jmol-users] BIG addition to Jmol -- CONTACT command

[Robert Hanson]

ps -- references at that bottom are to an alternative method of
visualization: We have incorporated into Jmol the "promolecular NCI" --
Noncovalent interactions -- calculation published recently in JACS[1] and
JCTC[2] by the Yang group at Duke. (The results of SCF NCIPLOT output are
also visualizable in Jmol using the isosurface command, but the CONTACT
command can be used as a simple way to check out and compare the NCI result
at least qualitatively.) But that's another story.

On Wed, Jun 22, 2011 at 3:03 AM, Robert Hanson  wrote:

> Jmol users --
>
> Not "big" as in lots of bytes, but BIG in terms of impact. I believe Erik
> Wyatt (undergraduate at St. Olaf) and I have cracked the nonbonding
> interations nut. With this announcement we hereby introduce what I just
> checked in as Jmol 12.1.51_dev: the CONTACT command. This new command
> displays objects that float in space between two interacting atoms. These
> could be hydrophobic interactions or hydrogen bonds or in principle any
> other interactions. A set of "teasers" can be found at
> http://stolaf.edu/people/hansonr/jmol/contact/2bxa.htm
>
> The objects created are similar to isosurfaces (and, in fact, are derived
> from them) and are created very efficiently and quickly. They can be
> rendered as flat planes perpendicular to the line connecting the interacting
> atoms, as cigar-shaped connections along those lines, and as volume-rendered
> dots. There are several adjustable parameters that allow fine-tuning the
> visualization to different sizes and contacts. They can be isolated very
> specifically to any set of atoms, and it appears so far to us that the
> presence of absence of hydrogen atoms does not make much of a difference.
> Thus, they can be implemented for any PDB, CIF, XYZ, or MOL files. All you
> need are some atoms.
>
> I predict these will be a big hit. These few examples will have to suffice
> for now.
>
> One question: Is anyone aware of anything like this in PyMOL or VMD or
> other packages?
>
> The CONTACT command is not at all limited to biomolecules, and I am hoping
> some people will give it a try with totally nonbiological systems.
>
> Just to give you a hint as to how they are created, it involves another new
> capability in Jmol 12.1.51: the ability to design any combination of two VDW
> surfaces based on any combining formula you can write into a Jmol math
> expression. As such, these objects were relatively easy to implement. Also
> important was a third new capability -- the capability to cleanly trim any
> mapped isosurface based on a range of values, including volume-rendered
> points. This is all now possible with the ISOSURFACE command and carried out
> using a much simplified syntax with the CONTACT command. For starters all
> you need to do is identify a ligand and enter:
>
>   contact {ligand}
>
> Then go from there. See 
> Jmol.propertiesfor
>  details.
>
> The CONTACT command will be in 12.1.51, which I hope we can release later
> this week. We do have a few more touches to add to this still. Looking to
> publish this by the end of the summer. For a possible figure in the paper
> and an acknowledgment, get your examples in early! We're very interested to
> see what people can do with these and what we need to do to make them
> especially useful.
>
> - Bob
>
> [1]
>  *   "Revealing Noncovalent Interactions",
>  *   Erin R. Johnson, Shahar Keinan, Paula Mori-Sanchez, Julia
> Contreras-Garcia, Aron J. Cohen, and Weitao Yang,
>  *   J. Am. Chem. Soc., 2010, 132, 6498-6506. email to
> julia.contre...@duke.edu
>
> [2]
>  *
>  *   "NCIPLOT: A Program for Plotting Noncovalent Interaction Regions"
>  *   Julia Contreras-García, Erin R. Johnson, Shahar Keinan, Robin
> Chaudret, Jean-Philip Piquemal, David N. Beratan, and Weitao Yang,
>  *   J. of Chemical Theory and Computation, 2011, 7, 625-632
>
>
> --
> 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 what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>



-- 
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 what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Simplify data backup and recovery for your virtual environment with vRanger.
Installation's a snap, and flexible recovery options mean your data is safe,
secure and there when you need it. Data protection magic?
Nope - It's vRanger. Get your free trial download today.
http://p.sf

[Jmol-users] BIG addition to Jmol -- CONTACT command

[Robert Hanson]

Jmol users --

Not "big" as in lots of bytes, but BIG in terms of impact. I believe Erik
Wyatt (undergraduate at St. Olaf) and I have cracked the nonbonding
interations nut. With this announcement we hereby introduce what I just
checked in as Jmol 12.1.51_dev: the CONTACT command. This new command
displays objects that float in space between two interacting atoms. These
could be hydrophobic interactions or hydrogen bonds or in principle any
other interactions. A set of "teasers" can be found at
http://stolaf.edu/people/hansonr/jmol/contact/2bxa.htm

The objects created are similar to isosurfaces (and, in fact, are derived
from them) and are created very efficiently and quickly. They can be
rendered as flat planes perpendicular to the line connecting the interacting
atoms, as cigar-shaped connections along those lines, and as volume-rendered
dots. There are several adjustable parameters that allow fine-tuning the
visualization to different sizes and contacts. They can be isolated very
specifically to any set of atoms, and it appears so far to us that the
presence of absence of hydrogen atoms does not make much of a difference.
Thus, they can be implemented for any PDB, CIF, XYZ, or MOL files. All you
need are some atoms.

I predict these will be a big hit. These few examples will have to suffice
for now.

One question: Is anyone aware of anything like this in PyMOL or VMD or other
packages?

The CONTACT command is not at all limited to biomolecules, and I am hoping
some people will give it a try with totally nonbiological systems.

Just to give you a hint as to how they are created, it involves another new
capability in Jmol 12.1.51: the ability to design any combination of two VDW
surfaces based on any combining formula you can write into a Jmol math
expression. As such, these objects were relatively easy to implement. Also
important was a third new capability -- the capability to cleanly trim any
mapped isosurface based on a range of values, including volume-rendered
points. This is all now possible with the ISOSURFACE command and carried out
using a much simplified syntax with the CONTACT command. For starters all
you need to do is identify a ligand and enter:

  contact {ligand}

Then go from there. See
Jmol.propertiesfor
details.

The CONTACT command will be in 12.1.51, which I hope we can release later
this week. We do have a few more touches to add to this still. Looking to
publish this by the end of the summer. For a possible figure in the paper
and an acknowledgment, get your examples in early! We're very interested to
see what people can do with these and what we need to do to make them
especially useful.

- Bob

[1]
 *   "Revealing Noncovalent Interactions",
 *   Erin R. Johnson, Shahar Keinan, Paula Mori-Sanchez, Julia
Contreras-Garcia, Aron J. Cohen, and Weitao Yang,
 *   J. Am. Chem. Soc., 2010, 132, 6498-6506. email to
julia.contre...@duke.edu

[2]
 *
 *   "NCIPLOT: A Program for Plotting Noncovalent Interaction Regions"
 *   Julia Contreras-García, Erin R. Johnson, Shahar Keinan, Robin Chaudret,
Jean-Philip Piquemal, David N. Beratan, and Weitao Yang,
 *   J. of Chemical Theory and Computation, 2011, 7, 625-632


-- 
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 what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Simplify data backup and recovery for your virtual environment with vRanger.
Installation's a snap, and flexible recovery options mean your data is safe,
secure and there when you need it. Data protection magic?
Nope - It's vRanger. Get your free trial download today.
http://p.sf.net/sfu/quest-sfdev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users