Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D
Very nice indeed! Bob, you are close to forcing me to upgrade the version of Jmol I am now using. Bill On Apr 11, 2010, at 12:52 AM, Robert Hanson wrote: OK! Here we go! Super simple 2D to 3D. The JME-Jmol connection has gone unused for too long. With today's 12.0.RC5 addition of reading bond stereochemistry, Jmol now does a pretty decent job of translating 2D into 3D -- admittedly this is not going to solve all problems, but give it a try: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm Cool, eh? Bob -- 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 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol Virtual Model Kit
Otis. Super. I don't think my latest jme reader will have that problem with planar rings. I have the z coordinate given a bit of noise. Keep playing with it. Some boats are probably inevitable. Sent from my iPhone On Apr 10, 2010, at 8:59 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, I have it set up on my home server. I'm only working with small molecules, but I haven't had a clunker yet. Wow, I am impressed! I actually took the stereo bonds off of the JME on the chemagic site. I need to put them back. I'm still going to bypass some other misses. For example, most users would simply draw cyclohexane as JME planar - no stereo bonds. UFF keeps that planar, so I'll just use the unique SMILES to reroute to a direct load from a cyclohexane chair file. Otis On 4/10/2010 6:41 PM, Robert Hanson wrote: Hey, check this out: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm 124. JME reader reads stereochemistry and automatically turns 2D to 3D with addition of H atoms The JME format is a two-dimensional file format that is easy to generate but not easily adapted to 3D. Jmol 12.0.RC5 adds the automatic addition of H atoms and transformation of simple JME structures (including stereochemistry) to 3D. The transfer is not perfect, and it may take some testing to get this right. Bob On Sat, Apr 10, 2010 at 4:22 PM, Robert Hanson hans...@stolaf.edu wrote: Otis, if you think it would be valuable, we could look into reading the stereochemistry of bonds and at least shifting a whole branch up or down an angstrom in the Z coordinate based on that. wouldn't be perfect, but it might not be that hard, either. As I started to do this, I realize that the JME reader is totally nonfunctional. I'm adding stereochemical reading, and it seems to work OK, but there is still a problem with the addhydrogens business. WIll fix On Fri, Apr 9, 2010 at 1:28 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bill, I'm passing molfiles from JME. Actually, the SMILES is also passed in the molfile (Name Position), but its the molfile that's rendered. The JME string might be worth a try. While the information is still 2D only, we have found that you can give UFF minimization good starts and bad starts based on the original 2D drawing. It's important to note that Jmol ignores stereo bonds from JME - only 2D info passed. Interestingly, it will pass formal charge information in the molfile, but the atom is not registered in Jmol as having the formal charge - i.e. the charges are only printed on the model. Otis On 4/9/2010 1:07 PM, william reusch wrote: Otis, Are you transferring the JME structure as a Smiles string or as a JME string. The latter has more information in it. Bill Otis Rothenberger wrote: Bill, Thanks for the comments. The 2D to 3D translation is an ongoing problem for us. The JME editor is light weight and it can be embedded directly in the application, but it passes only 2D information to Jmol. Jmol tries to sort this out with the UFF minimization. With really simple molecules this works, but there are serious limitations. We actually have two alternative options, and we need to discuss this in the users manual, a current high priority! --- --- --- - Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com --- --- --- - Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- 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
Re: [Jmol-users] [ jmol-Feature Requests-2985130 ] Display of charges
On 10 Apr 2010 at 18:53, Hans U Wagner wrote at SourceForge.net : Initial Comment: Hi, I didn't find any possibility to display formal charges of a molecule. One of our problem molecules is ozone O3. In our lectures we must use two mesomeric resonance formulas such as O(-) - O(+) = O - O = O(+) - O(-). How to display the formal charges, how the real symmetry of the molecule ? To my knowlegde there is only one program (available as applets) which can display such formulas, see attachement. But I want to use Jmol. We like ist because of the marvelous features. Is there any possibilty to add the formal charges to an atom in an molecule, such as in the attachement. Regards, Hans Hi Hans. I think there are several ways to do what you want, but more details will be useful to better direct you to a solution. First thoughts: 1. Jmol will read charges from several file formats, if they are there. 2. How do you expect to display the charges? As in your image, they would be Jmol labels. You can use label %C after selecting the desired atoms, and it will display formal charge. 3. You could also color by charge, use ionic radii, ... See 1. http://wiki.jmol.org/index.php/File_formats/Coordinates [serach for charge in there] 2. http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm#label -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] well, what do you know? Jmol and JME 2D to 3D
Yes, very cool and easy to use, perhaps too easy? My concern is the limitations of the minimisation which will lead to high energy minima. e.g. Cis decalin becomes chair-boat instead of chair-chair, biphenyl is flat, simple amides are not planar. This is not Jmol's fault per se but could be misleading. Otherwise works nicely. All the best Nick -- 3D Organic Animations http://www.chemtube3d.com Tel: +44 (0)151-794-3506 (3500 secretary) Subject: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D To: jmol-users@lists.sourceforge.net Message-ID: o2sba9c0bd61004102152r2848f768x43d726fab5e02...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 OK! Here we go! Super simple 2D to 3D. The JME-Jmol connection has gone unused for too long. With today's 12.0.RC5 addition of reading bond stereochemistry, Jmol now does a pretty decent job of translating 2D into 3D -- admittedly this is not going to solve all problems, but give it a try: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm Cool, eh? -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [ jmol-Feature Requests-2985130 ] Display of charges
Hello Hans,
Here is an additional approach that you can use if the formal charge
data is not in the coordinate file. You can assign the charges and
display them in the start up script:
{atomIndex = 1}.formalCharge = 2;color label pink;select formalCharge
0;label %C
I'm not sure which Jmol versions will work, but 11.9+ works.
Otis
On 4/11/2010 2:55 PM, Angel Herráez wrote:
On 10 Apr 2010 at 18:53, Hans U Wagner wrote at SourceForge.net :
Initial Comment:
Hi, I didn't find any possibility to display formal charges of a molecule.
One of our problem molecules is ozone O3. In our lectures we must use two
mesomeric resonance formulas such as O(-) - O(+) = O- O = O(+) - O(-).
How to display the formal charges, how the real symmetry of the molecule ?
To my knowlegde there is only one program (available as applets) which can
display such formulas, see attachement.
But I want to use Jmol. We like ist because of the marvelous features.
Is there any possibilty to add the formal charges to an atom in an molecule,
such as in the attachement.
Regards, Hans
Hi Hans.
I think there are several ways to do what you want, but more details will be
useful to better
direct you to a solution.
First thoughts:
1. Jmol will read charges from several file formats, if they are there.
2. How do you expect to display the charges? As in your image, they would
be Jmol
labels. You can use
label %C
after selecting the desired atoms, and it will display formal charge.
3. You could also color by charge, use ionic radii, ...
See
1. http://wiki.jmol.org/index.php/File_formats/Coordinates [serach for
charge in there]
2. http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm#label
--
Otis Rothenberger
chemagic.com
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Cannot open console
In 12.0.RC5_dev applet (at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm ) I cannot open the console. -Eric -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] RC4 crash: bondinfo
If I load 3kwb via Internet into 12.0.RC4, then enter getproperty bondinfo, it crashes. -Eric -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
