Re: [Jmol-users] Help with surfaces
I'm certainly not seeing that. I do see that they don't have the rwb colorscheme. So coming from the JVXL file you need to specify the color scheme: isosurface t2.jvxl colorscheme "rwb"* *I realize that should not be necessary, but it is. The color scheme used is not saved with the isosurface in a JVXL file. You mean they are not matching? I'm certainly not seeing that. See attached images. Bob On Wed, Feb 23, 2011 at 5:08 PM, Eduardo Oliveira wrote: > Hi Robert, > > Sorry it took me so long to answer. Your algorithm worked just fine, thank > you! > > However, i'm having another trouble now. After the surface is generated > everything is alright, i save it as a .jvxl file, then when i try to load it > to the same molecule, the surface and the molecule don't match, it seems > they have different coordinates. So i would like to know what i'm doing > wrong. > > > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-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 <><>-- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
Hi Robert, Sorry it took me so long to answer. Your algorithm worked just fine, thank you! However, i'm having another trouble now. After the surface is generated everything is alright, i save it as a .jvxl file, then when i try to load it to the same molecule, the surface and the molecule don't match, it seems they have different coordinates. So i would like to know what i'm doing wrong. -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Finally! A nice cyclohexane chair/chair flip demo
Henry, so you are saying you think something is wrong with that pathway. >From what I can see, there are two possible pathways from the chair -- one with a twist to the "left"; one with a twist to the "right." The enatiomeric twist is not depicted. (Although I think you could invert the configuration of all models and see it!) So from the get-go, symmetry is broken. Nothing wrong with that The entire sequence is chiral! Bob On Wed, Feb 23, 2011 at 1:29 PM, Rzepa, Henry wrote: > >Hens! Good to hear from you. I hope you don't mind my co-opting your model > -- reminds me that I need to put a link to WeTChe there. > > > >I'd love a little discusson of this, because I'd like to get this out > there. My understanding is that both are "correct" -- the boat transition > state is lower than the twist chair (though I don't see exactly why) > > > Because the angles are opened up beyond 109 in the half chair > > >, and so statistically the molecule will find itself more often in a boat > than a twist chair anyway, I think the "synthetic organic chemist" should > realize that what is > >shown is not a potential surface, but one degree of freedom singled out. > > > Surely a molecular dynamics trajectory is more accurate, since a degree of > freedom can only be harmonic and you cannot have harmonic modes connecting > the entire surface? The MD trajectory seems to show a boat transition state > being involved at the half way point, not a twist boat minimum? > > My concern is that a single degree of freedom singled out does not marry > with group theory! > > > -- > > +44 (020) 7594 5774 (Voice); Blog: http://www.ch.ic.ac.uk/rzepa/blog/ > Dept. Chemistry, Imperial College London, SW7 2AZ, UK. > > (Voracious anti-spam filter in operation for received email. > If expected reply not received, please phone/fax). > > > > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-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 -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Grouping of arbitrary elements
Thanks a lot, Bob! Speaking on the application, it's an implementation of one spatial protein structure modeling approach. We need to draw some geometric figures (dodecahedron for instance) near the protein. Besides, we need an ability to rotate and to move figures by user. 21:35 Wednesday 23 February 2011 you wrote: > If you can make your polygon using atoms, you can move and rotate it > independently in quite interesting ways. That's actually a nice idea. Also, > though, you might consider using the PMESH command rather than DRAW. A > pmesh object can be rotated, and offset easily. One catch, I think, is > that if it has sharp edges (like a cube), you might get some odd shadings > that you don't get with the draw version. it wouldn't be hard at all to > add ROTATE to the DRAW command similarly to the way it was added recently > to the PMESH/ISOSURFACE command. > > What's your specific application, Evgeny? > > Bob > > On Tue, Feb 22, 2011 at 3:15 PM, Kalishenko Evgeny wrote: > > Thanks for the suggestion. > > But moving and rotation are exactly what I want :) > > So, maybe it is time to see aside a drawing pseudomolecule with personal > > atom > > type created in a program way? > > > > 22:32 Tuesday 22 February 2011 you wrote: > > > Just give them some common initial characters of their ID, for example: > > > > > > draw obj1_pt1 .. > > > draw obj1_pt2 .. > > > > > > and then refer to them as > > > > > > draw obj1_* > > > > > > But there isn't a way of rotating drawn objects, just moving them > > > (using OFFSET), and wild cards like that don't work with OFFSET. So > > > that's not exactly a solution. > > > > > > Bob > > > > > > On Mon, Feb 21, 2011 at 4:41 PM, Kalishenko Evgeny > > > > wrote: > > > > Hi, > > > > I've started using Jmol recently and found out useful ability to make > > > > groups > > > > of atoms or molecules. It is convinient to act with a set of groups, > > > > but > > > > > > when > > > > I try to draw not an atom or molecule but, for instance, a sphere and > > > > a line > > > > - I meet some difficulties. I need to rotate an arbitrary geometric > > > > figure near the protein. Can I combine arbitrary drawn objects (lines > > > > and points) into one new object? Am I right that scripting doesn't > > > > support this now? > > > > > > > > -- > > > > Regards, > > > > Evgeny Kalishenko > > > > - > > > > > > - Index, Search & Analyze Logs and other IT data in Real-Time > > > > with Splunk Collect, index and harness all the fast moving IT data > > > > generated by your applications, servers and devices whether > > > > physical, virtual or in the cloud. > > > > Deliver compliance at lower cost and gain new business insights. > > > > Free Software Download: http://p.sf.net/sfu/splunk-dev2dev > > > > ___ > > > > Jmol-users mailing list > > > > Jmol-users@lists.sourceforge.net > > > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > -- > > Regards, > > Open Source and Linux Laboratory (osll.spb.ru) > > Evgeny Kalishenko > > > > > > - > > - Free Software Download: Index, Search & Analyze Logs and other IT > > data in Real-Time with Splunk. Collect, index and harness all the fast > > moving IT data > > generated by your applications, servers and devices whether physical, > > virtual > > or in the cloud. Deliver compliance at lower cost and gain new business > > insights. http://p.sf.net/sfu/splunk-dev2dev > > ___ > > Jmol-users mailing list > > Jmol-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/jmol-users Regards, Open Source and Linux Laboratory (osll.spb.ru) Evgeny Kalishenko -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Finally! A nice cyclohexane chair/chair flip demo
>Hens! Good to hear from you. I hope you don't mind my co-opting your model -- >reminds me that I need to put a link to WeTChe there. > >I'd love a little discusson of this, because I'd like to get this out there. >My understanding is that both are "correct" -- the boat transition state is >lower than the twist chair (though I don't see exactly why) Because the angles are opened up beyond 109 in the half chair >, and so statistically the molecule will find itself more often in a boat than >a twist chair anyway, I think the "synthetic organic chemist" should realize >that what is >shown is not a potential surface, but one degree of freedom singled out. Surely a molecular dynamics trajectory is more accurate, since a degree of freedom can only be harmonic and you cannot have harmonic modes connecting the entire surface? The MD trajectory seems to show a boat transition state being involved at the half way point, not a twist boat minimum? My concern is that a single degree of freedom singled out does not marry with group theory! -- +44 (020) 7594 5774 (Voice); Blog: http://www.ch.ic.ac.uk/rzepa/blog/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Grouping of arbitrary elements
If you can make your polygon using atoms, you can move and rotate it independently in quite interesting ways. That's actually a nice idea. Also, though, you might consider using the PMESH command rather than DRAW. A pmesh object can be rotated, and offset easily. One catch, I think, is that if it has sharp edges (like a cube), you might get some odd shadings that you don't get with the draw version. it wouldn't be hard at all to add ROTATE to the DRAW command similarly to the way it was added recently to the PMESH/ISOSURFACE command. What's your specific application, Evgeny? Bob On Tue, Feb 22, 2011 at 3:15 PM, Kalishenko Evgeny wrote: > Thanks for the suggestion. > But moving and rotation are exactly what I want :) > So, maybe it is time to see aside a drawing pseudomolecule with personal > atom > type created in a program way? > > 22:32 Tuesday 22 February 2011 you wrote: > > Just give them some common initial characters of their ID, for example: > > > > draw obj1_pt1 .. > > draw obj1_pt2 .. > > > > and then refer to them as > > > > draw obj1_* > > > > But there isn't a way of rotating drawn objects, just moving them (using > > OFFSET), and wild cards like that don't work with OFFSET. So that's not > > exactly a solution. > > > > Bob > > > > On Mon, Feb 21, 2011 at 4:41 PM, Kalishenko Evgeny > wrote: > > > Hi, > > > I've started using Jmol recently and found out useful ability to make > > > groups > > > of atoms or molecules. It is convinient to act with a set of groups, > but > > > when > > > I try to draw not an atom or molecule but, for instance, a sphere and a > > > line > > > - I meet some difficulties. I need to rotate an arbitrary geometric > > > figure near the protein. Can I combine arbitrary drawn objects (lines > > > and points) into one new object? Am I right that scripting doesn't > > > support this now? > > > > > > -- > > > Regards, > > > Evgeny Kalishenko > > > > > > > > > > - > > > - Index, Search & Analyze Logs and other IT data in Real-Time with > > > Splunk Collect, index and harness all the fast moving IT data generated > > > by your applications, servers and devices whether physical, virtual or > > > in the cloud. > > > Deliver compliance at lower cost and gain new business insights. > > > Free Software Download: http://p.sf.net/sfu/splunk-dev2dev > > > ___ > > > Jmol-users mailing list > > > Jmol-users@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- > Regards, > Open Source and Linux Laboratory (osll.spb.ru) > Evgeny Kalishenko > > > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-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 -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Finally! A nice cyclohexane chair/chair flip demo
Hens! Good to hear from you. I hope you don't mind my co-opting your model -- reminds me that I need to put a link to WeTChe there. I'd love a little discusson of this, because I'd like to get this out there. My understanding is that both are "correct" -- the boat transition state is lower than the twist chair (though I don't see exactly why), and so statistically the molecule will find itself more often in a boat than a twist chair anyway, whether you consider the boat a "dead end" or not; what you miss in the standard 2D representation is that the system does not HAVE to go through the boat, and can instead smoothly transition between the two chairs without it. One of the interesting things I've found is that this particular pathway is fun to demonstrate. See this lousy-resolution YouTube video, for instance: http://www.youtube.com/watch?v=38YKPG1r30Q If you do this, you can actually FEEL in your hands the model going over the twist-chair transition state, because all you are doing is pressing with the palm sides of your thumbs, and as soon as the transition state is passed, the model stops pushing back, and just sort of slides into place. In terms of Jmol, what is interesting here is that we can use the COMPARE command to align frames that otherwise would be difficult to align. Hens, did you ever think about aligning the frames this way? Bob On Wed, Feb 23, 2011 at 7:06 AM, Hens Borkent wrote: > > > Op 23-2-2011 10:12, Rzepa Henry schreef: > > > > > > I appreciate a debate on this topic may or may not be suited for the > > Jmol list, but if anyone wants to add their opinion, I would welcome > > this, if only because my "synthetic organic chemistry" colleagues > > need to know what the "most realistic" description of this iconic > > potential surface is! > > > I think the "synthetic organic chemist" should realize that what is > shown is not a potential surface, but one degree of freedom singled out. > To put it crudely: the molecule is wobbling all the time, hopping from > one possible path to the other, distorting any symmetry all the time. > More realistic, although not so appealing maybe as the animations shown. > My original was based on a series MOPAC IRC calculations starting from > selected transition state maxima. > Hens > > > > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-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 -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol version 12.x.xx and water molecule surface problem
Please try the latest upload of http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip I recently discovered Jmol wasn't extracting charge info from Spartan files; this should be fixed for the next release and I think is there already in that zip file version. Thanks, Bob On Wed, Feb 23, 2011 at 9:13 AM, Johannes Pernaa < johannes.per...@edumendo.fi> wrote: > Hi all. > > I have a problem with water molecule electrostatic potential surface in > latest Jmol versions. > > *Example:* > When I try visualize them using Jmol 11.x.xx versions, everything works > fine, but 12.x.xx versions won't show it. > > All other molecules works just fine in 12.x.xx versions. Water molecule is > the only one that I can't get to work. I have tried .spartan and mol.2 file > types (see attachment). > > Can anyone help me? > > Best regards > Johannes Pernaa > > > > > -- > Johannes Pernaa > Chairman of the board, Ph. Lic. > Edumendo - Advanced Learning and Visualization > Pasilanraitio 4 A 15 > 00240 Helsinki, Finland > E-mail: johannes.per...@edumendo.fi > Telephone: +358 44 700 8031 > Webpage: www.edumendo.fi > > > > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-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 -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol version 12.x.xx and water molecule surface problem
Johannes- I'm afraid I can't help, but I can confirm what your seeing: 1) Your file does not display MEP in 12.1.35. 2) A water molecule mol2 file that I created in Accelrys does not display MEP in 12.1.35 3) A water molecule Spartan file not display MEP in 12.1.35 4) The following PubChem file DOES display MEP http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=962&disopt=3DDisplay SDF Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org From: "Johannes Pernaa" Sent: Wednesday, February 23, 2011 11:06 AM To: jmol-users@lists.sourceforge.net Subject: [Jmol-users] Jmol version 12.x.xx and water molecule surface problem Hi all. I have a problem with water molecule electrostatic potential surface in latest Jmol versions. Example: When I try visualize them using Jmol 11.x.xx versions, everything works fine, but 12.x.xx versions won't show it. All other molecules works just fine in 12.x.xx versions. Water molecule is the only one that I can't get to work. I have tried .spartan and mol.2 file types (see attachment). Can anyone help me? Best regards Johannes Pernaa -- Johannes Pernaa Chairman of the board, Ph. Lic. Edumendo - Advanced Learning and Visualization Pasilanraitio 4 A 15 00240 Helsinki, Finland E-mail: johannes.per...@edumendo.fi Telephone: +358 44 700 8031 Webpage: www.edumendo.fi -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol version 12.x.xx and water molecule surface problem
Hi all. I have a problem with water molecule electrostatic potential surface in latest Jmol versions. *Example:* When I try visualize them using Jmol 11.x.xx versions, everything works fine, but 12.x.xx versions won't show it. All other molecules works just fine in 12.x.xx versions. Water molecule is the only one that I can't get to work. I have tried .spartan and mol.2 file types (see attachment). Can anyone help me? Best regards Johannes Pernaa -- Johannes Pernaa Chairman of the board, Ph. Lic. Edumendo - Advanced Learning and Visualization Pasilanraitio 4 A 15 00240 Helsinki, Finland E-mail: johannes.per...@edumendo.fi Telephone: +358 44 700 8031 Webpage: www.edumendo.fi water.mol2 Description: chemical/mol2 -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Finally! A nice cyclohexane chair/chair flip demo
Op 23-2-2011 10:12, Rzepa Henry schreef: > > > I appreciate a debate on this topic may or may not be suited for the > Jmol list, but if anyone wants to add their opinion, I would welcome > this, if only because my "synthetic organic chemistry" colleagues > need to know what the "most realistic" description of this iconic > potential surface is! > I think the "synthetic organic chemist" should realize that what is shown is not a potential surface, but one degree of freedom singled out. To put it crudely: the molecule is wobbling all the time, hopping from one possible path to the other, distorting any symmetry all the time. More realistic, although not so appealing maybe as the animations shown. My original was based on a series MOPAC IRC calculations starting from selected transition state maxima. Hens -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Finally! A nice cyclohexane chair/chair flip demo
On 23 Feb 2011, at 01:33, Robert Hanson wrote: > Well, at least I think so > > http://chemapps.stolaf.edu/jmol/docs/examples-12/jmol-flot-energy.htm?model=data/cyclohexaneFlip.jmol > > Please let me know if that does not work for you. Bob, The issue of whether the path passes through a boat transition state or not is an interesting one. The pathway you show is chiral at all points except the first and the last (D3d symmetry there, with planes of symmetry). In particular, point 18, the twist boat and the half way point, is itself chiral (C2 symmetry). The half chair transition states (10 and 25) are also chiral, but 10 is the enantiomer of 25. The alternative, shown in many texts, is of a mirror-symmetric potential, involving an achiral boat transition state (C2v) at the mid point, with the left of the potential a mirror image of the right. Thus we have chair-chair interconversion happening via either a pathway which has a mirror symmetric geometry at its mid point, or via a pathway which is chiral at every point except the start and end. This latter type of potential has been described by Patrick Fowler as "chiral connectedness" (although it does not quite match). See Symmetry: Culture and Science, Vol. 16, No 4, 321-334, 2005. An animation which purports to be derived from a molecular dynamics simulation can be seen at http://www.youtube.com/user/DokeDJ#p/u/4/bPLREpfZ63I and it does seem to support the intermediacy of a boat transition state at the "mid point" rather than passing directly from a twist boat to the half chair on one side of the potential. What I am trying to find here is whether the species either side of the mid point should be symmetric at each point of the potential or not. http://www.youtube.com/user/DokeDJ#p/u/4/bPLREpfZ63I seems to show this, but > http://chemapps.stolaf.edu/jmol/docs/examples-12/jmol-flot-energy.htm?model=data/cyclohexaneFlip.jmol does not. I appreciate a debate on this topic may or may not be suited for the Jmol list, but if anyone wants to add their opinion, I would welcome this, if only because my "synthetic organic chemistry" colleagues need to know what the "most realistic" description of this iconic potential surface is! -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Grouping of arbitrary elements
Evgeny,
Yes, you can add dummy atoms using a script. See
http://www.mail-archive.com/jmol-
us...@lists.sourceforge.net/msg16573.html
for some more info and an example.
You should best use the existing "Xx" notation for an undefined
element. Then you can "select Xx" to act on it, set its size, color,
etc.
Points and lines can be drawn giving their position with atom IDs,
but I'm afraid when you rotate the atoms the drawn objects will not
follow them, you would have to redraw. So you will have to resort to
using the dummy atom itself as a sphere and the bonds you define
(using "connect" command) as lines. Those will rotate
("rotateselected" command").
Not too straightforward, but possible.
Good luck
--
Free Software Download: Index, Search & Analyze Logs and other IT data in
Real-Time with Splunk. Collect, index and harness all the fast moving IT data
generated by your applications, servers and devices whether physical, virtual
or in the cloud. Deliver compliance at lower cost and gain new business
insights. http://p.sf.net/sfu/splunk-dev2dev
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