Re: [Jmol-users] Marvin Sketch

[Otis Rothenberger]

I should mention that the page also has a "ChemSketch" link. This link
simply does an inline molfile load of a molfile pasted in the page's
text field.

A Marvin Beans "View Source" as molfile can be copy pasted into the
field. It's not as slick as an auto transfer, but clicking the
"ChemSketch" link followed by Clicking the UFF link gets the job done
for the Marvin Beans structure in the text field.

Otis

On Fri, Jan 15, 2010 at 8:01 PM, Otis Rothenberger  wrote:
> Bob,
>
> I have a page that does this with the JME drawing applet. I'm not sure
> if this will help:
>
> http://chemagic.com/web_molecules/script_page_large.aspx
>
> The Draw Structure link opens the JME editor. The Load Structure sends
> the molfile to Jmol. While I have a UFF link on the page, the Load
> Structure link automatically runs the UFF on the loaded structure.
>
> Hope this helps.
>
> Otis
>
>
>
>
> On Fri, Jan 15, 2010 at 2:01 PM, Robert Hanson  wrote:
>> Does anyone have a page that we can play with that would allow Marvin input
>> of 2D structures and Jmol rendering of them in 3D?
>>
>> --
>> 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
>>
>> --
>> Throughout its 18-year history, RSA Conference consistently attracts the
>> world's best and brightest in the field, creating opportunities for
>> Conference
>> attendees to learn about information security's most important issues
>> through
>> interactions with peers, luminaries and emerging and established companies.
>> http://p.sf.net/sfu/rsaconf-dev2dev
>>
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
>
> --
> Otis Rothenberger
> http://chemagic.org
>



-- 
Otis Rothenberger
http://chemagic.org

--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
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Re: [Jmol-users] browser hanging again

[Grossman, Robert B]

Bob, your late-night efforts appear not to have been in vain.  With the 
Jmol-11.zip folder you reference below, my browser no longer crashes.  I did 
not even use the ?JMOLJAR formulation in my URL.

Let's hope you've solved the problem for good now.

-- Bob


On 1/15/10 7:28 PM, "Robert Hanson"  wrote:

Ah, OK. I spent almost all last night (I mean ALL) fixing this nasty bug. I 
introduced it into both Jmol 11.8 and 11.9 last month, I'm afraid. Should be 
fixed in Jmol 11.8.17 and Jmol 11.9.19, both ready for release.

Please try the Jar files in 
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip and see if that 
fixes it. You can do this by using your link with the following appended:

?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar

Or at least that might work. Also, please send the link that crashes. Always 
fun to try to fix those. not.

Bob



On Fri, Jan 15, 2010 at 3:37 PM, Grossman, Robert B  
wrote:
Hi,

Jmol is consistently hanging my browser (Safari and Firefox both) when I 
display a particular page.

It's a page in which I display a list of 13 questions.  The page contains about 
one figure per question, all of which are JPEGs, except one question has a Jmol 
applet.

However, when I display a page with a list of 3 questions, the browser does not 
hang.  I'm showing the same Jmol content (or nearly so) in the two pages.

The only difference between the two pages that I can see is that in the one 
that hangs, the Jmol applet is off the end of the screen.   I can't imagine 
that would be enough to make Jmol hang, but maybe I'm wrong.

The HTML of the two pages is posted at 
http://epoch.chem.uky.edu/epoch-plugin/public/questionsList.jsp1.txt (doesn't 
crash the browser) and 
http://epoch.chem.uky.edu/epoch-plugin/public/questionsList.jsp2.txt (crashes 
the browser).  Search for jmolApplet to find the call to Jmol.

Any insight you could offer would be appreciated.

-- Bob G.

--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
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Re: [Jmol-users] "could not find applet jmolApplet0"

[Grossman, Robert B]

This one's not a hanging offense, but I started using script tags for my Jmol 
applets because I may have more than one per page, and each time I load a page 
now, I get an alert saying, "could not find applet jmolApplet0".  It appears to 
be of no consequence, because the applets, whether there's one or more, load 
fine.  At first I was naming my applets jmolApplet1, jmolAppet2, etc., so I 
changed them to jmolApplet0, etc., but I still get the message.

Here's the relevant part of the code:


var jmolMol0 = '\n  Marvin  03180516593D\n\n 22 
22  0  0  0  0999 V2000\n   -0.42010.2577   -1.4146 C   0  0  0 
 0  0  0  0  0  0  6  0  0\n1.01190.6024   -0.9257 C   0  0  2  0  0  0 
 0  0  0  5  0  0\n1.4430   -0.31570.2489 C   0  0  2  0  0  0  0  0  0 
 4  0  0\n0.4201   -0.25771.4146 C   0  0  0  0  0  0  0  0  0  3  0  
0\n   -1.0119   -0.60240.9257 C   0  0  0  0  0  0  0  0  0  2  0  0\n   
-1.44300.3157   -0.2489 C   0  0  0  0  0  0  0  0  0  1  0  0\n   -0.7193  
  0.9460   -2.2082 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4212   -0.7482 
  -1.8450 H   0  0  0  0  0  0  0  0  0  0  0  0\n1.72070.5093   
-1.7516 H   0  0  0  0  0  0  0  0  0  0  0  0\n1.5221   -1.3462   -0.1098 
H   0  0  0  0  0  0  0  0  0  0  0  0\n0.7193   -0.94602.2082 H   0  0 
 0  0  0  0  0  0  0  0  0  0\n0.42120.74821.8450 H   0  0  0  0  0 
 0  0  0  0  0  0  0\n   -1.7207   -0.50931.7516 H   0  0  0  0  0  0  0  0 
 0  0  0  0\n   -1.0386   -1.64540.5961 H   0  0  0  0  0  0  0  0  0  0  0 
 0\n   -1.52211.34620.1098 H   0  0  0  0  0  0  0  0  0  0  0  0\n   
-2.43310.0241   -0.6065 H   0  0  0  0  0  0  0  0  0  0  0  0\n2.8389  
  0.09540.7531 C   0  0  0  0  0  0  0  0  0  0  0  0\n1.04952.0704 
  -0.4618 C   0  0  0  0  0  0  0  0  0  0  0  0\n2.38322.8404   
-0.4618 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.27422.8574   -0.4618 
C   0  0  0  0  0  0  0  0  0  0  0  0\n4.1725   -0.67460.7531 C   0  0 
 0  0  0  0  0  0  0  0  0  0\n5.4409   -0.01771.3286 C   0  0  0  0  0 
 0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  1  6  1  0  0  0  0\n  2  3  1  
0  0  0  0\n  3  4  1  0  0  0  0\n  4  5  1  0  0  0  0\n  5  6  1  0  0  0  
0\n  1  7  1  0  0  0  0\n  1  8  1  0  0  0  0\n  2  9  1  0  0  0  0\n  2 18  
1  0  0  0  0\n  3 17  1  0  0  0  0\n  3 10  1  0  0  0  0\n  4 11  1  0  0  0 
 0\n  4 12  1  0  0  0  0\n  5 13  1  0  0  0  0\n  5 14  1  0  0  0  0\n  6 15 
 1  0  0  0  0\n  6 16  1  0  0  0  0\n 17 21  1  0  0  0  0\n 18 19  1  0  0  
0  0\n 18 20  1  0  0  0  0\n 21 22  1  0  0  0  0\nM  END\n';
var bgcolor = 'white';
var height = 250;
var width = 250;
var addlScripts = 'set spin y 20;  ';



// 




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Re: [Jmol-users] Marvin Sketch

[Otis Rothenberger]

Bob,

I have a page that does this with the JME drawing applet. I'm not sure
if this will help:

http://chemagic.com/web_molecules/script_page_large.aspx

The Draw Structure link opens the JME editor. The Load Structure sends
the molfile to Jmol. While I have a UFF link on the page, the Load
Structure link automatically runs the UFF on the loaded structure.

Hope this helps.

Otis




On Fri, Jan 15, 2010 at 2:01 PM, Robert Hanson  wrote:
> Does anyone have a page that we can play with that would allow Marvin input
> of 2D structures and Jmol rendering of them in 3D?
>
> --
> 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
>
> --
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for
> Conference
> attendees to learn about information security's most important issues
> through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
>
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>



-- 
Otis Rothenberger
http://chemagic.org

--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
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___
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Re: [Jmol-users] browser hanging again

[Robert Hanson]

Ah, OK. I spent almost all last night (I mean ALL) fixing this nasty bug. I
introduced it into both Jmol 11.8 and 11.9 last month, I'm afraid. Should be
fixed in Jmol 11.8.17 and Jmol 11.9.19, both ready for release.

Please try the Jar files in
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip and see if that
fixes it. You can do this by using your link with the following appended:

?JMOLJAR=
http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar

Or at least that might work. Also, please send the link that crashes. Always
fun to try to fix those. not.

Bob



On Fri, Jan 15, 2010 at 3:37 PM, Grossman, Robert B  wrote:

> Hi,
>
> Jmol is consistently hanging my browser (Safari and Firefox both) when I
> display a particular page.
>
> It's a page in which I display a list of 13 questions.  The page contains
> about one figure per question, all of which are JPEGs, except one question
> has a Jmol applet.
>
> However, when I display a page with a list of 3 questions, the browser does
> not hang.  I'm showing the same Jmol content (or nearly so) in the two
> pages.
>
> The only difference between the two pages that I can see is that in the one
> that hangs, the Jmol applet is off the end of the screen.   I can't imagine
> that would be enough to make Jmol hang, but maybe I'm wrong.
>
> The HTML of the two pages is posted at
> http://epoch.chem.uky.edu/epoch-plugin/public/questionsList.jsp1.txt(doesn't 
> crash the browser) and
> http://epoch.chem.uky.edu/epoch-plugin/public/questionsList.jsp2.txt(crashes 
> the browser).  Search for jmolApplet to find the call to Jmol.
>
> Any insight you could offer would be appreciated.
>
> -- Bob G.
>
>
> --
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for
> Conference
> attendees to learn about information security's most important issues
> through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-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
--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev___
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Re: [Jmol-users] Marvin Sketch

[Grossman, Robert B]

Do you mean that you want to draw a structure in Marvin and press a button to 
send it to Jmol?  I can probably put one together over the weekend, if no one 
has one ready.



From: Robert Hanson 
Reply-To: 
Date: Fri, 15 Jan 2010 14:01:20 -0500
To: 
Conversation: [Jmol-users] Marvin Sketch
Subject: [Jmol-users] Marvin Sketch

Does anyone have a page that we can play with that would allow Marvin input of 
2D structures and Jmol rendering of them in 3D?

--
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


--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
___
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[Jmol-users] browser hanging again

[Grossman, Robert B]

Hi,

Jmol is consistently hanging my browser (Safari and Firefox both) when I 
display a particular page.

It's a page in which I display a list of 13 questions.  The page contains about 
one figure per question, all of which are JPEGs, except one question has a Jmol 
applet.

However, when I display a page with a list of 3 questions, the browser does not 
hang.  I'm showing the same Jmol content (or nearly so) in the two pages.

The only difference between the two pages that I can see is that in the one 
that hangs, the Jmol applet is off the end of the screen.   I can't imagine 
that would be enough to make Jmol hang, but maybe I'm wrong.

The HTML of the two pages is posted at 
http://epoch.chem.uky.edu/epoch-plugin/public/questionsList.jsp1.txt (doesn't 
crash the browser) and 
http://epoch.chem.uky.edu/epoch-plugin/public/questionsList.jsp2.txt (crashes 
the browser).  Search for jmolApplet to find the call to Jmol.

Any insight you could offer would be appreciated.

-- Bob G.

--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
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[Jmol-users] Marvin Sketch

[Robert Hanson]

Does anyone have a page that we can play with that would allow Marvin input
of 2D structures and Jmol rendering of them in 3D?

-- 
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
--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev___
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Re: [Jmol-users] feature suggestions

[Robert Hanson]

We'll have to experiment. You could add some but not all -- just select the
atoms you want to add the hydrogens to. As implemented, Jmol will not add
MORE hydrogens to any atom already bearing hydrogens.

-- oh, the latest has formal charge added. I don't know about radicals.
Mostly we need to keep this very simple. Let's see what people can do with
it and then tweak it later. It would be nice if we just had a list of PDB
atom types and their number of H atoms to add. Someone must have that.

Angel, I'm starting to think the "Jmol 12.0" idea is a good one. A few
"quantum leaps" here, I think, since 11.0:

-- loads of cyrstallography-related features
-- full support for electron microscopy data (EfVET, CCP4, MRC, XPLOR)
-- new vertex/triangle-based surface readers
-- XML-based JVXL file format "XJVXL"
-- vertex/triangle compression in XJVXL

-- WebExport functionality in application
-- PovRAY, UDTF, X3D, VRML export
-- "live" JPG and PNG images with embedded Jmol state scripts

-- calculate AROMATIC
-- calculate HBONDS
-- calculate HYROGEN
-- calcuate POINTGROUP
-- calculate SURFACEDISTANCE
-- minimize (UFF calculation)
-- minimize addHydrogens

-- atom and model deletion

-- customizable boundbox, measures, and unit cells
-- scalable label and echo fonts
-- customizable Van der Waals radius
-- cube file subset reading
-- draw CIRCLE, LINE, VECTOR, POLYGON, and LINEDATA options
-- draw RAMACHANDRAN, FRAME, BOUNDBOX, UNITCELL options
-- draw INTERSECTION
-- isosurface CONTOURS
-- isosurface SCALE3D ("terrain" maps)
-- show/draw SYMOP
-- multifeatured anisotropic ellipsoid rendering
-- echo/background IMAGE

-- load TRAJECTORY
-- load FILTER
-- load FILTER "BIOMOLECULE..."
-- load support for filtered AMBER trajectories
-- load ZIP files as directory sets

-- select {atom expression} (boolean property expression)

-- loads of new SET parameters

--  script APPLET appletName "some script"
   for direct applet-applet communication
-- script LOCALPATH/REMOTEPATH/SCRIPTPATH options
-- write LOCALPATH/REMOTEPATH options

-- RAMACHANDRAN and QUATERNION commands

-- Java/JavaScript-like feel to scripting language
-- user-definable functions
-- easily settable atom properties
-- math support for points, planes, quaternions,
  atom sets, bond sets, matrices, arrays
-- user-definable color schemes
-- fully customizable menu
-- popup file dialog for signed applet
-- fully customizable mouse/action bindings

-- several new applet callbacks
-- applet synchronization
-- multi-touch

-- Chinese translation

This is a partial list, of course! Won't be any time soon, mind you.



2010/1/15 Angel Herráez 

> Robert Hanson escribió:
>
> > calculate hydrogen # adds the hydrogen atoms to C,N,O,and S atoms,
> > respecting bonding but not considering formal charge (for now).
>
> This sounds exciting, Bob!
>
>
> > minimize addHydrogens # minimizes and then adds H atoms at the end
>
>
> I have one wonder here. In my experience with 2D models, Jmol often
> minimizes non-H models badly (I was guessing if didn't have enough
> info*), but behaves well when I add the Hs (in another program)
> before minimizing.
> So, is it reasonable to add Hs after the minimization, or maybe
> before it?
>
> (*) for example, a cyclohexane remains hexagonal flat unless it has
> the Hs --an extreme case, but representative of others
>
>
>
>
> --
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for
> Conference
> attendees to learn about information security's most important issues
> through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-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
--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev___
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Re: [Jmol-users] feature suggestions

[Angel Herráez]

Robert Hanson escribió:

> calculate hydrogen # adds the hydrogen atoms to C,N,O,and S atoms, 
> respecting bonding but not considering formal charge (for now).

This sounds exciting, Bob!


> minimize addHydrogens # minimizes and then adds H atoms at the end


I have one wonder here. In my experience with 2D models, Jmol often 
minimizes non-H models badly (I was guessing if didn't have enough 
info*), but behaves well when I add the Hs (in another program) 
before minimizing. 
So, is it reasonable to add Hs after the minimization, or maybe 
before it?

(*) for example, a cyclohexane remains hexagonal flat unless it has 
the Hs --an extreme case, but representative of others



--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
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Re: [Jmol-users] feature suggestions

[rgb]

How do you decide on how pyramidal (or not) to make a N Bob? What about
hydroxyl H atoms when there is the potential for intramolecular H-bonding?

Rich

 On Fri, 15 Jan 2010 11:01:22 -0600, Robert Hanson 
wrote:
> OK, that's in.   See Jmol 11.9.19 ---
> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
> 
> calculate hydrogen   # adds the hydrogen atoms to C,N,O,and S atoms,
> respecting bonding but not considering formal charge (for now).
> 
> minimize addHydrogens  # minimizes and then adds H atoms at the end
> 
> delete {hydrogen}# does that
> 
> Bob
> 
> On Thu, Jan 14, 2010 at 9:14 PM, Grossman, Robert B
> > wrote:
> 
>> My suggestion would be that if a multiple bond is not specified, you
>> should
>> assume a single bond, and if a charge or radical is not specified, you
>> should assume enough H atoms to give the atom its octet.  If the user
is
>> not
>> specifying multiple bonds, then he simply shouldn't use the function.
>>
>> Consider the MOL file below.  Some H atoms are specified, some not.  I
>> had
>> Jmol do a minimization, and it correctly deplanarized the isopropyl
>> group.
>>  If it can do that, then it can easily position the H atoms.


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Re: [Jmol-users] multi-touch terminology: swipe

[Robert Hanson]

Both act the same in Jmol multiTouch.

swipe: put finger on surface, drag in a single direction, while continuing
> the drag motion lift finger from surface
>
> flick: swipe but done must faster
>
> :-)
>
> Rich
>
>
> --
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for
> Conference
> attendees to learn about information security's most important issues
> through
> interactions with peers, luminaries and emerging and established companies.
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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
--
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world's best and brightest in the field, creating opportunities for Conference
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Re: [Jmol-users] feature suggestions

[Robert Hanson]

Paul, also note that the Jmol state is incldued in those PNG or JPG files,
so you can just drag and drop them into Jmol or use

script "file.png"

There is an issue there with directory paths. The latest rendition of Jmol
strips all local paths off but leaves the web-based paths. when reading
these back in, if just the image, then the associated files need to be in
the directory of that image. But that can be over-ridden with

script LOCALPATH "path/for/local/refs" REMOTEPATH "path/for/remote/refs"
SCRIPTPATH "path/for/./refs" (these last created automatically for JPG and
PNG files)





On Thu, Jan 14, 2010 at 1:21 PM, Paul Pillot <
paul.pil...@ac-orleans-tours.fr> wrote:

>
> Le 14 janv. 2010 à 20:07, Grossman, Robert B a écrit :
>
> >
> >
> > (2) Save image of the current view.  The best format would be PNG.  Yes,
> I can do a screen capture of a view with another program, but that's extra
> work.
> >
> That feature exists. You've got two options :
> - using the signed applet, you can send the script
> save IMAGE PNG "filepath/imagename.png"
> - with the unsigned applet, use the getproperty method which sends a base64
> jpg string, from which you can make a regular file using a remote server
>
> Paul
>
>
> --
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for
> Conference
> attendees to learn about information security's most important issues
> through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> ___
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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
--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
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Re: [Jmol-users] feature suggestions

[Robert Hanson]

OK, that's in.   See Jmol 11.9.19 ---
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip

calculate hydrogen   # adds the hydrogen atoms to C,N,O,and S atoms,
respecting bonding but not considering formal charge (for now).

minimize addHydrogens  # minimizes and then adds H atoms at the end

delete {hydrogen}# does that

Bob

On Thu, Jan 14, 2010 at 9:14 PM, Grossman, Robert B  wrote:

> My suggestion would be that if a multiple bond is not specified, you should
> assume a single bond, and if a charge or radical is not specified, you
> should assume enough H atoms to give the atom its octet.  If the user is not
> specifying multiple bonds, then he simply shouldn't use the function.
>
> Consider the MOL file below.  Some H atoms are specified, some not.  I had
> Jmol do a minimization, and it correctly deplanarized the isopropyl group.
>  If it can do that, then it can easily position the H atoms.
>
>
>  Marvin  03180516593D
>
>  22 22  0  0  0  0999 V2000
>   -0.42010.2577   -1.4146 C   0  0  0  0  0  0  0  0  0  6  0  0
>1.01190.6024   -0.9257 C   0  0  2  0  0  0  0  0  0  5  0  0
>1.4430   -0.31570.2489 C   0  0  2  0  0  0  0  0  0  4  0  0
>0.4201   -0.25771.4146 C   0  0  0  0  0  0  0  0  0  3  0  0
>   -1.0119   -0.60240.9257 C   0  0  0  0  0  0  0  0  0  2  0  0
>   -1.44300.3157   -0.2489 C   0  0  0  0  0  0  0  0  0  1  0  0
>   -0.71930.9460   -2.2082 H   0  0  0  0  0  0  0  0  0  0  0  0
>   -0.4212   -0.7482   -1.8450 H   0  0  0  0  0  0  0  0  0  0  0  0
>1.72070.5093   -1.7516 H   0  0  0  0  0  0  0  0  0  0  0  0
>1.5221   -1.3462   -0.1098 H   0  0  0  0  0  0  0  0  0  0  0  0
>0.7193   -0.94602.2082 H   0  0  0  0  0  0  0  0  0  0  0  0
>0.42120.74821.8450 H   0  0  0  0  0  0  0  0  0  0  0  0
>   -1.7207   -0.50931.7516 H   0  0  0  0  0  0  0  0  0  0  0  0
>   -1.0386   -1.64540.5961 H   0  0  0  0  0  0  0  0  0  0  0  0
>   -1.52211.34620.1098 H   0  0  0  0  0  0  0  0  0  0  0  0
>   -2.43310.0241   -0.6065 H   0  0  0  0  0  0  0  0  0  0  0  0
>2.83890.09540.7531 C   0  0  0  0  0  0  0  0  0  0  0  0
>1.04952.0704   -0.4618 C   0  0  0  0  0  0  0  0  0  0  0  0
>2.38322.8404   -0.4618 C   0  0  0  0  0  0  0  0  0  0  0  0
>   -0.27422.8574   -0.4618 C   0  0  0  0  0  0  0  0  0  0  0  0
>4.1725   -0.67460.7531 C   0  0  0  0  0  0  0  0  0  0  0  0
>5.4409   -0.01771.3286 C   0  0  0  0  0  0  0  0  0  0  0  0
>  1  2  1  0  0  0  0
>  1  6  1  0  0  0  0
>  2  3  1  0  0  0  0
>  3  4  1  0  0  0  0
>  4  5  1  0  0  0  0
>  5  6  1  0  0  0  0
>  1  7  1  0  0  0  0
>  1  8  1  0  0  0  0
>  2  9  1  0  0  0  0
>  2 18  1  0  0  0  0
>  3 17  1  0  0  0  0
>  3 10  1  0  0  0  0
>  4 11  1  0  0  0  0
>  4 12  1  0  0  0  0
>  5 13  1  0  0  0  0
>  5 14  1  0  0  0  0
>  6 15  1  0  0  0  0
>  6 16  1  0  0  0  0
>  17 21  1  0  0  0  0
>  18 19  1  0  0  0  0
>  18 20  1  0  0  0  0
>  21 22  1  0  0  0  0
> M  END
>
>
>
> On 1/14/10 9:42 PM, "Robert Hanson"  wrote:
>
>
>
> On Thu, Jan 14, 2010 at 1:07 PM, Grossman, Robert B <
> robert.gross...@uky.edu> wrote:
> (1) Display H atoms.  If I load a structure that does not show H atoms, it
> would be nice to have Jmol calculate their positions and display them.  I
> know it must know that they are there, because when I loaded a structure
> with a planar C the the center of an isopropyl group, then minimized the
> structure, it converted the C to tetrahedral.  (I guess it's possible you
> have this feature, but I'm not able to find it.)
>
> Jmol doesn't know they are there. The UFF calculation is simply optimizing
> the single-bond C-framework.  If the problem can be better defined, we might
> be able to do something about it. Certainly would be a good trick. Do you
> have the bonding already -- double, triple? One problem, for example, is:
>
> C -C-O
>
> is that CH3CH2OH? CH2CH2OH? CH2C=O? CH3CHO? If the bonding is there, then
> we are ok; if it is not, then
>
> But if you have double bonds, it's easy. Send me a file.
>
> Bob
>
>
>
> --
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for
> Conference
> attendees to learn about information security's most important issues
> through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-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 

Re: [Jmol-users] Happy New Year -- some interesting new features for Jmol 11.9.17

[Robert Hanson]

Jmol 11.9.18 -- Now this can be more easily displayed:

display configuration=1
display configuration=2

On Mon, Jan 11, 2010 at 10:11 AM, Robert Hanson  wrote:

> Jmol reads the occupancy into the altloc parameter provided the CIF file
> has alternate sites indicated.
>
> select altloc=1
> select altloc=2
> configuration 1;display selected
> configuration 2;display selected
>
> etc.
>
>
>
>
> On Mon, Jan 11, 2010 at 9:47 AM, Phillip Barak  wrote:
>
>> - Original Message -
>> From: Robert Hanson 
>> Date: Sunday, January 10, 2010 1:24 am
>> Subject: [Jmol-users] Happy New Year -- some interesting new features for
>>   Jmol 11.9.17
>> To: jmol-users@lists.sourceforge.net
>>
>> >...
>> > I'm working on crystallography this month. So if you have ideas in that
>> > regard, do speak up...
>>
>> Many cif files have occupancy fields, which indicate that a given spot is
>> occupied only x% of the time. Jmol currently, to the best of my
>> understanding, ignores the occupancy info and populates all of those spots.
>> I'm not exactly sure what Jmol or other molecular visualization _should_ do
>> with such info except to automagically populate some and not others by some
>> routine to come up to the desired occupancy level. Anyone else have thoughts
>> on the subject?
>>
>> --Phillip Barak
>> Univ of Wisconsin-Madison
>>
>> p.s.: many thanks to Bob for the outstanding work over these past 5 yrs!
>> The entire Jmol community is grateful.
>>
>>
>> --
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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
>



-- 
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
--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev___
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Re: [Jmol-users] Subscription problem - help please

[Nicolas Vervelle]

Hi Eric,

Strange, I don't see your subscription with your yahoo mail address...
I have invited you, you should receive a mail to confirm that you want to
subscribe.
If it doesn't work, I can directly add your second subscription.

Nico

On Fri, Jan 15, 2010 at 8:00 AM, Eric Martz wrote:

> I attempted to subscribe to jmol-users two days ago but have received
> no confirmation nor any messages from the list at the new address
> (nor in the spam box). I want a second subscription at
> martze...@yahoo.com because I cannot use my main email
> ema...@microbio.umass.edu inside the Weizmann Institute, because they
> block POP mail. Until the new subscription works, I can only access
> the list from my apartment outside the Weizmann, mornings and evenings.
>
> Yes, Bob, I am working on electron density maps. I will communicate
> as soon as I have something to show. Thanks for the info you have provided.
>
> -Eric
>
> 
> Eric Martz, Professor Emeritus, Dept Microbiology
> University of Massachusetts, Amherst MA US
> http://Martz.MolviZ.Org 
>
>
>
> --
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for
> Conference
> attendees to learn about information security's most important issues
> through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> ___
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
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