Re: [Jmol-users] Atom Replacement Problem
Wow, Otis. You are doing some very interesting things here! OK, I will look
into it. Sounds like the minimization routine isn't using the correct atom
locations.
On Thu, Feb 11, 2010 at 7:36 PM, Otis Rothenberger o...@chemagic.comwrote:
Hello-
I'm using the following JavaScript to replace univalent atoms is a Jmol
model:
evalRasmol(if ({atomIndex= + atomIndex + }.valence =1){{atomIndex= +
atomIndex + }.element = ' + buildAtom + '; wireframe 0.15; spacefill
20%;minimize addHydrogens;boundbox {*};select *;center selected;});
With atomIndex = 1 and buildAtom = Cl, for example, the evalRasmol
function is processing the following Jmol script:
if ({atomIndex=1}.valence =1){{atomIndex=1}.element = Cl; wireframe 0.15;
spacefill 20%;minimize addHydrogens;boundbox {*};select *;center selected;}
This all works very nicely, including a new bond length, for one
substitution. After that, the substitution is made, but the bond length
remains unchanged.
Again by way of example, methane changes smoothly to chloromethane. While
the next substitution leads to methylene chloride, the methylene chloride
has one normal C-Cl bond length and one C-Cl bond length equal to a C-H bond
length.
In summary, for a wide range of molecules, the above process works well
once. After that, bond length for the added atom is not changed.
The following variation of the above JavaScript leads to the same result:
evalRasmol(if ({atomIndex= + atomIndex + }.valence
=1){{atomIndex= + atomIndex + }.element = ' + buildAtom + '; wireframe
0.15; spacefill 20%;minimize addHydrogens;});
The following variation makes it clear that it is the spacefill command
that adjusts the added atoms vdw, and it is the minimize command that
adjusts the bond length. But only once
evalRasmol(if ({atomIndex= + atomIndex + }.valence
=1){{atomIndex= + atomIndex + }.element = ' + buildAtom + ';});
Does anyone have any suggestions that might allow subsequent substitutions
to behave as the first? As a point of information the JavaScript is
initiated by a click callback when the univalent atom is clicked.
Otis
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If nature does not answer first what we want,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Atom Replacement Problem
Well, Otis, I'm guessing you will have a full-fledged Jmol-based molecular
editor for us soon. Is that right?
This is fixed for Jmol 11.9.29. See
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
Bob
[PS: I'm not sure I would do the center selected there -- doesn't that
result in an odd jump? I think it would be cooler to just let the model
relax as you change the atoms.]
On Thu, Feb 11, 2010 at 7:36 PM, Otis Rothenberger o...@chemagic.comwrote:
Hello-
I'm using the following JavaScript to replace univalent atoms is a Jmol
model:
evalRasmol(if ({atomIndex= + atomIndex + }.valence =1){{atomIndex= +
atomIndex + }.element = ' + buildAtom + '; wireframe 0.15; spacefill
20%;minimize addHydrogens;boundbox {*};select *;center selected;});
With atomIndex = 1 and buildAtom = Cl, for example, the evalRasmol
function is processing the following Jmol script:
if ({atomIndex=1}.valence =1){{atomIndex=1}.element = Cl; wireframe 0.15;
spacefill 20%;minimize addHydrogens;boundbox {*};select *;center selected;}
This all works very nicely, including a new bond length, for one
substitution. After that, the substitution is made, but the bond length
remains unchanged.
Again by way of example, methane changes smoothly to chloromethane. While
the next substitution leads to methylene chloride, the methylene chloride
has one normal C-Cl bond length and one C-Cl bond length equal to a C-H bond
length.
In summary, for a wide range of molecules, the above process works well
once. After that, bond length for the added atom is not changed.
The following variation of the above JavaScript leads to the same result:
evalRasmol(if ({atomIndex= + atomIndex + }.valence
=1){{atomIndex= + atomIndex + }.element = ' + buildAtom + '; wireframe
0.15; spacefill 20%;minimize addHydrogens;});
The following variation makes it clear that it is the spacefill command
that adjusts the added atoms vdw, and it is the minimize command that
adjusts the bond length. But only once
evalRasmol(if ({atomIndex= + atomIndex + }.valence
=1){{atomIndex= + atomIndex + }.element = ' + buildAtom + ';});
Does anyone have any suggestions that might allow subsequent substitutions
to behave as the first? As a point of information the JavaScript is
initiated by a click callback when the univalent atom is clicked.
Otis
--
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http://chemagic.org
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St. Olaf College
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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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Re: [Jmol-users] Atom Replacement Problem
valency accounts for bond order. So just about every carbon will be
tetravalent, regardless of is position in a molecule -- acetylene, ethene,
ethane all have {_C}.valence = 4. But if there are only three single bonds
to a carbon, its valence will be reported as 3.
By the way, Otis -- you will have more bugs to report. No one has done much
with this, and I think you are going to find more places where Jmol doesn't
do what you expect it to do. Just keep reporting these.
Bob
2010/2/12 Angel Herráez angel.herr...@uah.es
Sorry, Otis, I cannot help with your problem (but the feature looks
exciting! One more step towards a Jmol editor, even if a simple one.)
Your post prompts a question: is this valency property a shortcut
meaning number of bonds? Bob?
--
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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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Re: [Jmol-users] Atom Replacement Problem
Bob and Angel-
Thanks for the help and the words of encouragement. My objective is to
create the Jmol equivalent of an old Prentice Hall Model Kit, and a
molecular builder (editor, I guess) is part of this objective.
At present, I only know how to build molecules in Jmol using univalent atoms
as a spring board via replacement. I have users start with methane, ethene,
ethyne, or methanal. They can then click/change any univalent atom to C, H,
O, X, or N. Your newly added minimize does the rest. I said it before, and
I'll say it again: for folks interested in small molecules, this was a super
addition to Jmol.
I'd love to build C directly onto C (i.e. actually add a C, O, N etc.), but
I'm not sure how to proceed. If you can point me on this, I'd appreciate it.
The clean up at the end of my current routine is really not bad visually. I
had to do it to keep the growing molecule in the window, especially when
adding methyl groups:
http://chemagic.com/web_molecules/script_page_large.aspx
Other Points:
1) atomno's are duplicated during this building process (i.e. during the
addHydrogens step). That's why I used atomIndex.
2) Holding addHydrogens until the end of several changes fixes the bond
length issue. Unfortunately, it also eliminates the hydrogens as sequential
handles for further chain growth.
3) Question: Is there a way to strip H's and then add them back in?
Otis
On Fri, Feb 12, 2010 at 6:30 AM, Robert Hanson hans...@stolaf.edu wrote:
valency accounts for bond order. So just about every carbon will be
tetravalent, regardless of is position in a molecule -- acetylene, ethene,
ethane all have {_C}.valence = 4. But if there are only three single bonds
to a carbon, its valence will be reported as 3.
By the way, Otis -- you will have more bugs to report. No one has done much
with this, and I think you are going to find more places where Jmol doesn't
do what you expect it to do. Just keep reporting these.
Bob
2010/2/12 Angel Herráez angel.herr...@uah.es
Sorry, Otis, I cannot help with your problem (but the feature looks
exciting! One more step towards a Jmol editor, even if a simple one.)
Your post prompts a question: is this valency property a shortcut
meaning number of bonds? Bob?
--
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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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
--
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
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http://chemagic.org
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Re: [Jmol-users] Atom Replacement Problem
Otis wrote: If you are after a web application, I don't think there's an alternative, but do you know Avogadro? It's an app, lets you build 3D molecules in real time. The clean up at the end of my current routine is really not bad visually. I had to do it to keep the growing molecule in the window, especially when adding methyl groups: Maybe instead of center you can use a smoothed command like zoomTo that will do the same but along some interval. In fact, center may eb able to do the same, both commands share a lot lately. 3) Question: Is there a way to strip H's and then add them back in? There is a way to delete atoms, is there not? So you should be able to use that for all Hs. But I'm not sure, I don't delete atoms every day ;) Does not minimize just reposition the Hs? -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Atom Replacement Problem
It seems that minimize does not work after set picking deleteatom has been used -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Atom Replacement Problem
Bob and Angel- This is all coming together very nicely. I did not know about the delete atom command. Using delete hydrogen; minimize addHydrogens after each atom replacement allows a wide range of editing moves, including extending the click/change to non-univalent atoms. The changes that you made to minimize addHydrogens have also corrected the bond length problem. Thanks again for the help. Otis 2010/2/12 Angel Herráez angel.herr...@uah.es It seems that minimize does not work after set picking deleteatom has been used -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger http://chemagic.org -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Atom Replacement Problem
Have a methyl radical precalculated as data. Merge it; translate/rotate it
to align it. Add the bond. A good challenge.
On Fri, Feb 12, 2010 at 1:06 PM, Otis Rothenberger o...@chemagic.comwrote:
Bob and Angel-
Thanks for the help and the words of encouragement. My objective is to
create the Jmol equivalent of an old Prentice Hall Model Kit, and a
molecular builder (editor, I guess) is part of this objective.
At present, I only know how to build molecules in Jmol using univalent
atoms as a spring board via replacement. I have users start with methane,
ethene, ethyne, or methanal. They can then click/change any univalent atom
to C, H, O, X, or N. Your newly added minimize does the rest. I said it
before, and I'll say it again: for folks interested in small molecules, this
was a super addition to Jmol.
I'd love to build C directly onto C (i.e. actually add a C, O, N etc.), but
I'm not sure how to proceed. If you can point me on this, I'd appreciate it.
The clean up at the end of my current routine is really not bad visually. I
had to do it to keep the growing molecule in the window, especially when
adding methyl groups:
http://chemagic.com/web_molecules/script_page_large.aspx
Other Points:
1) atomno's are duplicated during this building process (i.e. during the
addHydrogens step). That's why I used atomIndex.
2) Holding addHydrogens until the end of several changes fixes the bond
length issue. Unfortunately, it also eliminates the hydrogens as sequential
handles for further chain growth.
3) Question: Is there a way to strip H's and then add them back in?
Otis
On Fri, Feb 12, 2010 at 6:30 AM, Robert Hanson hans...@stolaf.edu wrote:
valency accounts for bond order. So just about every carbon will be
tetravalent, regardless of is position in a molecule -- acetylene, ethene,
ethane all have {_C}.valence = 4. But if there are only three single bonds
to a carbon, its valence will be reported as 3.
By the way, Otis -- you will have more bugs to report. No one has done
much with this, and I think you are going to find more places where Jmol
doesn't do what you expect it to do. Just keep reporting these.
Bob
2010/2/12 Angel Herráez angel.herr...@uah.es
Sorry, Otis, I cannot help with your problem (but the feature looks
exciting! One more step towards a Jmol editor, even if a simple one.)
Your post prompts a question: is this valency property a shortcut
meaning number of bonds? Bob?
--
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
http://p.sf.net/sfu/solaris-dev2dev
___
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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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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
--
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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Re: [Jmol-users] Atom Replacement Problem
hint: see http://chemapps.stolaf.edu/quaternions/jmol/helix.htm
On Fri, Feb 12, 2010 at 9:25 PM, Robert Hanson hans...@stolaf.edu wrote:
Have a methyl radical precalculated as data. Merge it; translate/rotate it
to align it. Add the bond. A good challenge.
On Fri, Feb 12, 2010 at 1:06 PM, Otis Rothenberger o...@chemagic.comwrote:
Bob and Angel-
Thanks for the help and the words of encouragement. My objective is to
create the Jmol equivalent of an old Prentice Hall Model Kit, and a
molecular builder (editor, I guess) is part of this objective.
At present, I only know how to build molecules in Jmol using univalent
atoms as a spring board via replacement. I have users start with methane,
ethene, ethyne, or methanal. They can then click/change any univalent atom
to C, H, O, X, or N. Your newly added minimize does the rest. I said it
before, and I'll say it again: for folks interested in small molecules, this
was a super addition to Jmol.
I'd love to build C directly onto C (i.e. actually add a C, O, N etc.),
but I'm not sure how to proceed. If you can point me on this, I'd appreciate
it.
The clean up at the end of my current routine is really not bad visually.
I had to do it to keep the growing molecule in the window, especially when
adding methyl groups:
http://chemagic.com/web_molecules/script_page_large.aspx
Other Points:
1) atomno's are duplicated during this building process (i.e. during the
addHydrogens step). That's why I used atomIndex.
2) Holding addHydrogens until the end of several changes fixes the bond
length issue. Unfortunately, it also eliminates the hydrogens as sequential
handles for further chain growth.
3) Question: Is there a way to strip H's and then add them back in?
Otis
On Fri, Feb 12, 2010 at 6:30 AM, Robert Hanson hans...@stolaf.eduwrote:
valency accounts for bond order. So just about every carbon will be
tetravalent, regardless of is position in a molecule -- acetylene, ethene,
ethane all have {_C}.valence = 4. But if there are only three single bonds
to a carbon, its valence will be reported as 3.
By the way, Otis -- you will have more bugs to report. No one has done
much with this, and I think you are going to find more places where Jmol
doesn't do what you expect it to do. Just keep reporting these.
Bob
2010/2/12 Angel Herráez angel.herr...@uah.es
Sorry, Otis, I cannot help with your problem (but the feature looks
exciting! One more step towards a Jmol editor, even if a simple one.)
Your post prompts a question: is this valency property a shortcut
meaning number of bonds? Bob?
--
SOLARIS 10 is the OS for Data Centers - provides features such as
DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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___
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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
--
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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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
--
SOLARIS 10
Re: [Jmol-users] Atom Replacement Problem
I thought I fixed that. 2010/2/12 Angel Herráez angel.herr...@uah.es It seems that minimize does not work after set picking deleteatom has been used -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-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 -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
