Re: [Jmol-users] smol files
On 6/30/2010 4:50 PM, Robert Hanson wrote: I'm not having that problem at all with my Spartan files. I look at a vibration: frame 3; vibration on then go back to frame 1 and check the MO: frame 1; MO HOMO Works fine. Certainly Jmol is never no longer able to access Frame 1. Maybe you are just not going back to frame 1? I have incorrectly assumed that turning off vibrations restores model 1 (one with surface data). I think I understand the logic behind this behavior now. [...] I have a Spartan question: How do you construct an energy profile plot that allows you to easily correlate specific conformations to specific energies (as for example with butane)? I can do that in Sygress/CaCHE or using Spartan files with my Jmol/Google plot page, but is there some way of doing that directly in Spartan? Bob I am guessing that you would like to have a clickable (or otherwise interactive) graph linking (let's say) energy values with specific conformers. I do not know how to do that. Spartan provides a convenient spreadsheet function that allows one to collect energy data as a function of torsional angle and plot them (or even fit the data). A demonstration case is in the Spartan 08 Tutorial and User Guide (p. 98). PM -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
about Spartan -- I guess I'll stick with http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm You can just drag and drop any Spartan file into that applet, and it will display the associated clickable graph. Hopefully they will get a feature such as this into some future edition of Spartan Student. For now this will have to do. I don't see spreadsheets very appealing unless there is a direct clickable interface between their data and the actual conformation. It's the connection between the specific energies and the specific conformations that my students need to make, not so much the overall energy picture. Bob I have a Spartan question: How do you construct an energy profile plot that allows you to easily correlate specific conformations to specific energies (as for example with butane)? I can do that in Sygress/CaCHE or using Spartan files with my Jmol/Google plot page, but is there some way of doing that directly in Spartan? Bob I am guessing that you would like to have a clickable (or otherwise interactive) graph linking (let's say) energy values with specific conformers. I do not know how to do that. Spartan provides a convenient spreadsheet function that allows one to collect energy data as a function of torsional angle and plot them (or even fit the data). A demonstration case is in the Spartan 08 Tutorial and User Guide (p. 98). PM -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
Bob, You can do this in Spartan. For example, make a butane molecule and create a dihedral angle constraint. Display the properties window and click on the dihedral angle constraint to show the properties for it. Set it to vary from -180 to 180. Set up an Energy Profile calculation and run it. When it is done, close the original butane molecule so only the results of the Energy Profile calculation are showing. Select the dihedral angle. At the bottom right of the screen, next to where it shows the value of the angle should be a letter P in a yellow box. Click on it. It should enter the dihedral angle values into the spreadsheet. You can also enter values for the energies in whatever units you want or the relative energy (it will set the lowest energy to zero). Now go to the Display menu and choose Plots... Make sure the Properties checkbox is checked. Choose Constraint from the X-axis popup and whatever energy you want from the list for the Y-axis then click OK. This is all in the Mac version. Might be a little different on the Windows version. But it definitely will do it and it isn't too hard. Jeff *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jul 1, 2010, at 12:37 PM, Robert Hanson wrote: about Spartan -- I guess I'll stick with http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm You can just drag and drop any Spartan file into that applet, and it will display the associated clickable graph. Hopefully they will get a feature such as this into some future edition of Spartan Student. For now this will have to do. I don't see spreadsheets very appealing unless there is a direct clickable interface between their data and the actual conformation. It's the connection between the specific energies and the specific conformations that my students need to make, not so much the overall energy picture. Bob I have a Spartan question: How do you construct an energy profile plot that allows you to easily correlate specific conformations to specific energies (as for example with butane)? I can do that in Sygress/CaCHE or using Spartan files with my Jmol/Google plot page, but is there some way of doing that directly in Spartan? Bob I am guessing that you would like to have a clickable (or otherwise interactive) graph linking (let's say) energy values with specific conformers. I do not know how to do that. Spartan provides a convenient spreadsheet function that allows one to collect energy data as a function of torsional angle and plot them (or even fit the data). A demonstration case is in the Spartan 08 Tutorial and User Guide (p. 98). PM -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
It's actually not that hard to do. No you don't have to enter each dihedral individually into the spreadsheet and yes you can click on any point on the graph and show the corresponding conformation. The hardest part is actually getting the conformations and their energies and it sounds like you already know how to do that. I could show you, but I'm leaving town tomorrow so it would have to wait until I get back. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jul 1, 2010, at 3:08 PM, Robert Hanson wrote: I guess I'll have to have somebody show me how that works. If this produces the same result as http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm? -- I mean you can click on any point on the graph, and the corresponding conformation is displayed, that's great. Still, it seems rather involved. Do you have to enter each dihedral individually into the spreadsheet? Bob On Thu, Jul 1, 2010 at 1:22 PM, Jeff Hansen jhan...@depauw.edu wrote: Bob, You can do this in Spartan. For example, make a butane molecule and create a dihedral angle constraint. Display the properties window and click on the dihedral angle constraint to show the properties for it. Set it to vary from -180 to 180. Set up an Energy Profile calculation and run it. When it is done, close the original butane molecule so only the results of the Energy Profile calculation are showing. Select the dihedral angle. At the bottom right of the screen, next to where it shows the value of the angle should be a letter P in a yellow box. Click on it. It should enter the dihedral angle values into the spreadsheet. You can also enter values for the energies in whatever units you want or the relative energy (it will set the lowest energy to zero). Now go to the Display menu and choose Plots... Make sure the Properties checkbox is checked. Choose Constraint from the X-axis popup and whatever energy you want from the list for the Y-axis then click OK. This is all in the Mac version. Might be a little different on the Windows version. But it definitely will do it and it isn't too hard. Jeff *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jul 1, 2010, at 12:37 PM, Robert Hanson wrote: about Spartan -- I guess I'll stick with http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm You can just drag and drop any Spartan file into that applet, and it will display the associated clickable graph. Hopefully they will get a feature such as this into some future edition of Spartan Student. For now this will have to do. I don't see spreadsheets very appealing unless there is a direct clickable interface between their data and the actual conformation. It's the connection between the specific energies and the specific conformations that my students need to make, not so much the overall energy picture. Bob I have a Spartan question: How do you construct an energy profile plot that allows you to easily correlate specific conformations to specific energies (as for example with butane)? I can do that in Sygress/CaCHE or using Spartan files with my Jmol/Google plot page, but is there some way of doing that directly in Spartan? Bob I am guessing that you would like to have a clickable (or otherwise interactive) graph linking (let's say) energy values with specific conformers. I do not know how to do that. Spartan provides a convenient spreadsheet function that allows one to collect energy data as a function of torsional angle and plot them (or even fit the data). A demonstration case is in the Spartan 08 Tutorial and User Guide (p. 98). PM -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the
Re: [Jmol-users] smol files
On 6/29/2010 7:20 PM, Robert Hanson wrote: I'll look into the mep/mo business. Should not be a problem. Just a bug, I think. Thank you very much for your help. I do have two related questions: 1. Can more than one surface be read from these files by Jmol? 2. Can Jmol write jvxl files with multiple surfaces? Since I have just started learning Jmol and have noticed the incredible amount of work you have put into this project, I would like to take this opportunity to express my thanks for your contribution to the development of such an invaluable tool for organic chemists. PM On Mon, Jun 28, 2010 at 7:45 AM, Pshemak Maslak p...@chem.psu.edu mailto:p...@chem.psu.edu wrote: On 6/25/2010 4:51 PM, Greeves, Nick wrote: I have used smol files for vibration e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well without any server side settings. All the best Nick Sent from my iPad Thank you very much for the example. Your case indeed clarifies the behavior: vibration and surfaces (mep and MOs) appear to be mutually exclusive with smol files, and if you do not reload, you cannot access the surfaces. Try the following: start any of the vibrations. Now stop it (check the vibration check box twice). Now check if MO's are still in the menu and what kind mep loads (not the one form smol, but one generated by Jmol). This is exactly what I was trying to explain (I am new to Jmol). That issue was not related to the MIME type question (although both were about smol). The same happens on the desktop Jmol. Thank you for your assistance. PM -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first http://sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto: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 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
When Jmol reads a Spartan smol file, it accesses all vibrations and all molecular orbitals (supposedly!) They should be accessible via the right-click menu (or by clicking the Jmol logo). MOs are under surfaces; vibrations are under model (at the top). Each vibration is another frame or model, and generally one of those models has the MOs. For some readers that is the first model, some the second, some the last. It all depends upon the reader. With Spartan, the MOs should be in model 1, and the vibrations should be the models after that. Makes sure you have issued vibration on if you want to see the vibrations or using that menu, Vibration-ON http://chemapps.stolaf.edu/jmol/docs/examples-11/data/C6H6.smol should be a good example of this. Bob On Wed, Jun 30, 2010 at 6:19 AM, Pshemak Maslak p...@chem.psu.edu wrote: On 6/29/2010 7:20 PM, Robert Hanson wrote: I'll look into the mep/mo business. Should not be a problem. Just a bug, I think. Thank you very much for your help. I do have two related questions: 1. Can more than one surface be read from these files by Jmol? 2. Can Jmol write jvxl files with multiple surfaces? Since I have just started learning Jmol and have noticed the incredible amount of work you have put into this project, I would like to take this opportunity to express my thanks for your contribution to the development of such an invaluable tool for organic chemists. PM On Mon, Jun 28, 2010 at 7:45 AM, Pshemak Maslak p...@chem.psu.edu wrote: On 6/25/2010 4:51 PM, Greeves, Nick wrote: I have used smol files for vibration e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well without any server side settings. All the best Nick Sent from my iPad Thank you very much for the example. Your case indeed clarifies the behavior: vibration and surfaces (mep and MOs) appear to be mutually exclusive with smol files, and if you do not reload, you cannot access the surfaces. Try the following: start any of the vibrations. Now stop it (check the vibration check box twice). Now check if MO's are still in the menu and what kind mep loads (not the one form smol, but one generated by Jmol). This is exactly what I was trying to explain (I am new to Jmol). That issue was not related to the MIME type question (although both were about smol). The same happens on the desktop Jmol. Thank you for your assistance. PM -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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 -- -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first -- ___ Jmol-users mailing listjmol-us...@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
On 6/30/2010 9:32 AM, Robert Hanson wrote: When Jmol reads a Spartan smol file, it accesses all vibrations and all molecular orbitals (supposedly!) They should be accessible via the right-click menu (or by clicking the Jmol logo). MOs are under surfaces; vibrations are under model (at the top). Thanks. I am new to Jmol, but not that new. :-) I have no problems individually visualizing any of the vibrations, or MOs, or mep surfaces from smol files.. The problem (possibly a bug as you have suggested) is that once vibrations are visualized the MOs or mep are no longer accessible without reloading the smol file. I am guessing that the frame that holds MO and mep data is not longer read by Jmol after one of the vibrational frames was read. For example, after stopping vibrations (vibration off) MO # would give a message that no MO coefficient data is available for this frame, and no MO is displayed. When I choose all vibrational frames (from the menu) I get the same error message, but the MO loads! Each vibration is another frame or model, and generally one of those models has the MOs. For some readers that is the first model, some the second, some the last. It all depends upon the reader. With Spartan, the MOs should be in model 1, and the vibrations should be the models after that. Makes sure you have issued vibration on if you want to see the vibrations or using that menu, Vibration-ON http://chemapps.stolaf.edu/jmol/docs/examples-11/data/C6H6.smol should be a good example of this. Bob Coming back to my related questions: Can any other surfaces (in addition to MOs and mep) be visualized through smol files? Can Jmol write jvxl files with multiple surfaces (for example selected MOs)? Thanks for all your help. PM On Wed, Jun 30, 2010 at 6:19 AM, Pshemak Maslak p...@chem.psu.edu mailto:p...@chem.psu.edu wrote: On 6/29/2010 7:20 PM, Robert Hanson wrote: I'll look into the mep/mo business. Should not be a problem. Just a bug, I think. Thank you very much for your help. I do have two related questions: 1. Can more than one surface be read from these files by Jmol? 2. Can Jmol write jvxl files with multiple surfaces? Since I have just started learning Jmol and have noticed the incredible amount of work you have put into this project, I would like to take this opportunity to express my thanks for your contribution to the development of such an invaluable tool for organic chemists. PM On Mon, Jun 28, 2010 at 7:45 AM, Pshemak Maslak p...@chem.psu.edu mailto:p...@chem.psu.edu wrote: On 6/25/2010 4:51 PM, Greeves, Nick wrote: I have used smol files for vibration e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well without any server side settings. All the best Nick Sent from my iPad Thank you very much for the example. Your case indeed clarifies the behavior: vibration and surfaces (mep and MOs) appear to be mutually exclusive with smol files, and if you do not reload, you cannot access the surfaces. Try the following: start any of the vibrations. Now stop it (check the vibration check box twice). Now check if MO's are still in the menu and what kind mep loads (not the one form smol, but one generated by Jmol). This is exactly what I was trying to explain (I am new to Jmol). That issue was not related to the MIME type question (although both were about smol). The same happens on the desktop Jmol. Thank you for your assistance. PM -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first http://sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto: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 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first http://sprint.com/first --
Re: [Jmol-users] smol files
Just to clarify. It sounds like the problem Pshemak is having is that when he looks at the vibrations, it is actually switching to another frame or model. These other frames or models do not contain the MOs. The MOs are still there (associated with the first model - or is model 1 the second model?). To see the MOs along with the other models I suppose they could be copied over using some javascript? However, it seems this would look funny with some static MO with the atoms moving relative to it. If what Pshemak wants is to animate through the vibration models and have an MO associated with each vibration model which has been calculated for that model that will be a tough thing to do. It is no longer a Jmol issue but rather how to get Spartan to calculate an MO for each vibration model it is generating then output that in a way that Jmol could read and animate. Probably possible, but I'm not sure exactly how to do it. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jun 30, 2010, at 9:32 AM, Robert Hanson wrote: When Jmol reads a Spartan smol file, it accesses all vibrations and all molecular orbitals (supposedly!) They should be accessible via the right-click menu (or by clicking the Jmol logo). MOs are under surfaces; vibrations are under model (at the top). Each vibration is another frame or model, and generally one of those models has the MOs. For some readers that is the first model, some the second, some the last. It all depends upon the reader. With Spartan, the MOs should be in model 1, and the vibrations should be the models after that. Makes sure you have issued vibration on if you want to see the vibrations or using that menu, Vibration-ON http://chemapps.stolaf.edu/jmol/docs/examples-11/data/C6H6.smol should be a good example of this. Bob On Wed, Jun 30, 2010 at 6:19 AM, Pshemak Maslak p...@chem.psu.edu wrote: On 6/29/2010 7:20 PM, Robert Hanson wrote: I'll look into the mep/mo business. Should not be a problem. Just a bug, I think. Thank you very much for your help. I do have two related questions: 1. Can more than one surface be read from these files by Jmol? 2. Can Jmol write jvxl files with multiple surfaces? Since I have just started learning Jmol and have noticed the incredible amount of work you have put into this project, I would like to take this opportunity to express my thanks for your contribution to the development of such an invaluable tool for organic chemists. PM On Mon, Jun 28, 2010 at 7:45 AM, Pshemak Maslak p...@chem.psu.edu wrote: On 6/25/2010 4:51 PM, Greeves, Nick wrote: I have used smol files for vibration e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well without any server side settings. All the best Nick Sent from my iPad Thank you very much for the example. Your case indeed clarifies the behavior: vibration and surfaces (mep and MOs) appear to be mutually exclusive with smol files, and if you do not reload, you cannot access the surfaces. Try the following: start any of the vibrations. Now stop it (check the vibration check box twice). Now check if MO's are still in the menu and what kind mep loads (not the one form smol, but one generated by Jmol). This is exactly what I was trying to explain (I am new to Jmol). That issue was not related to the MIME type question (although both were about smol). The same happens on the desktop Jmol. Thank you for your assistance. PM -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net email is sponsored by Sprint What
Re: [Jmol-users] smol files
On 6/30/2010 10:38 AM, Jeff Hansen wrote: OK. So ignore my previous post. I was thinking you wanted to view the vibrations and MOs simultaneously. Obviously not what you want. You said that MO # gives a message that no MO coefficient data is available. This would be true unless you are in model 1. I think just stopping vibrations will leave you in whichever model was showing when you stopped vibrations. Unless that happened to be the first model then you wouldn't have any MOs available. Switch to model 1 and the MOs should be available. What other surfaces are you interested in? Thanks. I think your comments helped me to figure out how that works. There is no bug: it is how it is designed: one has to (manually i.e. through menu or script) return back to the frame with MO info. As you have said stopping vibration does not automatically return Jmol to frame (model) 1 (where MO's are). I am mostly interested in setting Jmol in such a way that is easily accesiblke to students. I do not want the Jmol mechanics to divert from the chemistry contents. Since Spartan easily calculates various surfaces (density(bonds), density(HOMO) or density(LUMO to name the few, I was wandering if they are written into smol files and whether they are accessible through Jmol. Thanks! PM. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu mailto:jhan...@depauw.edu *** On Jun 30, 2010, at 10:27 AM, Pshemak Maslak wrote: On 6/30/2010 9:32 AM, Robert Hanson wrote: When Jmol reads a Spartan smol file, it accesses all vibrations and all molecular orbitals (supposedly!) They should be accessible via the right-click menu (or by clicking the Jmol logo). MOs are under surfaces; vibrations are under model (at the top). Thanks. I am new to Jmol, but not that new. :-) I have no problems individually visualizing any of the vibrations, or MOs, or mep surfaces from smol files.. The problem (possibly a bug as you have suggested) is that once vibrations are visualized the MOs or mep are no longer accessible without reloading the smol file. I am guessing that the frame that holds MO and mep data is not longer read by Jmol after one of the vibrational frames was read. For example, after stopping vibrations (vibration off) MO # would give a message that no MO coefficient data is available for this frame, and no MO is displayed. When I choose all vibrational frames (from the menu) I get the same error message, but the MO loads! Each vibration is another frame or model, and generally one of those models has the MOs. For some readers that is the first model, some the second, some the last. It all depends upon the reader. With Spartan, the MOs should be in model 1, and the vibrations should be the models after that. Makes sure you have issued vibration on if you want to see the vibrations or using that menu, Vibration-ON http://chemapps.stolaf.edu/jmol/docs/examples-11/data/C6H6.smol should be a good example of this. Bob Coming back to my related questions: Can any other surfaces (in addition to MOs and mep) be visualized through smol files? Can Jmol write jvxl files with multiple surfaces (for example selected MOs)? Thanks for all your help. PM On Wed, Jun 30, 2010 at 6:19 AM, Pshemak Maslak p...@chem.psu.edu mailto:p...@chem.psu.edu wrote: On 6/29/2010 7:20 PM, Robert Hanson wrote: I'll look into the mep/mo business. Should not be a problem. Just a bug, I think. Thank you very much for your help. I do have two related questions: 1. Can more than one surface be read from these files by Jmol? 2. Can Jmol write jvxl files with multiple surfaces? Since I have just started learning Jmol and have noticed the incredible amount of work you have put into this project, I would like to take this opportunity to express my thanks for your contribution to the development of such an invaluable tool for organic chemists. PM On Mon, Jun 28, 2010 at 7:45 AM, Pshemak Maslak p...@chem.psu.edu mailto:p...@chem.psu.edu wrote: On 6/25/2010 4:51 PM, Greeves, Nick wrote: I have used smol files for vibration e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well without any server side settings. All the best Nick Sent from my iPad Thank you very much for the example. Your case indeed clarifies the behavior: vibration and surfaces (mep and MOs) appear to be mutually exclusive with smol files, and if you do not reload, you cannot access the surfaces. Try the following: start any of the vibrations. Now stop it (check the vibration check box twice). Now check if MO's are still in
Re: [Jmol-users] smol files
Glad that helped. Making it easily accessible to students means doing most of the work for them. In the case of Jmol that means setting up buttons or checkboxes or whatever user interface then scripting what you want the students to see. In the case of viewing the MOs or some other surface you could create a button which the students would click to show the surface. Would be easy enough to include in that script a command to return to model 1 so the MOs would be available to view. Those surfaces in Spartan are basically the electron density surface colored according to other properties. Jmol will certainly allow you to visualize the electron density surface. My understanding is that you can also color it by whatever property you want. There would be some serious scripting involved in doing this. Without knowing exactly what is in the smol file, I would imagine the data for those properties are there somewhere. you would have to grab that data somehow then instruct Jmol to use it as the basis for coloring the surface. I'm no expert on this, but perhaps someone else can help with the details of this. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jun 30, 2010, at 2:09 PM, Pshemak Maslak wrote: On 6/30/2010 10:38 AM, Jeff Hansen wrote: OK. So ignore my previous post. I was thinking you wanted to view the vibrations and MOs simultaneously. Obviously not what you want. You said that MO # gives a message that no MO coefficient data is available. This would be true unless you are in model 1. I think just stopping vibrations will leave you in whichever model was showing when you stopped vibrations. Unless that happened to be the first model then you wouldn't have any MOs available. Switch to model 1 and the MOs should be available. What other surfaces are you interested in? Thanks. I think your comments helped me to figure out how that works. There is no bug: it is how it is designed: one has to (manually i.e. through menu or script) return back to the frame with MO info. As you have said stopping vibration does not automatically return Jmol to frame (model) 1 (where MO's are). I am mostly interested in setting Jmol in such a way that is easily accesiblke to students. I do not want the Jmol mechanics to divert from the chemistry contents. Since Spartan easily calculates various surfaces (density(bonds), density(HOMO) or density(LUMO to name the few, I was wandering if they are written into smol files and whether they are accessible through Jmol. Thanks! PM. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jun 30, 2010, at 10:27 AM, Pshemak Maslak wrote: On 6/30/2010 9:32 AM, Robert Hanson wrote: When Jmol reads a Spartan smol file, it accesses all vibrations and all molecular orbitals (supposedly!) They should be accessible via the right-click menu (or by clicking the Jmol logo). MOs are under surfaces; vibrations are under model (at the top). Thanks. I am new to Jmol, but not that new. :-) I have no problems individually visualizing any of the vibrations, or MOs, or mep surfaces from smol files.. The problem (possibly a bug as you have suggested) is that once vibrations are visualized the MOs or mep are no longer accessible without reloading the smol file. I am guessing that the frame that holds MO and mep data is not longer read by Jmol after one of the vibrational frames was read. For example, after stopping vibrations (vibration off) MO # would give a message that no MO coefficient data is available for this frame, and no MO is displayed. When I choose all vibrational frames (from the menu) I get the same error message, but the MO loads! Each vibration is another frame or model, and generally one of those models has the MOs. For some readers that is the first model, some the second, some the last. It all depends upon the reader. With Spartan, the MOs should be in model 1, and the vibrations should be the models after that. Makes sure you have issued vibration on if you want to see the vibrations or using that menu, Vibration-ON http://chemapps.stolaf.edu/jmol/docs/examples-11/data/C6H6.smol should be a good example of this. Bob Coming back to my related questions: Can any other surfaces (in addition to MOs and mep) be visualized through smol files? Can Jmol write jvxl files with multiple surfaces (for example selected MOs)? Thanks for all your help. PM On Wed, Jun 30, 2010 at 6:19 AM, Pshemak Maslak p...@chem.psu.edu wrote: On 6/29/2010 7:20 PM,
Re: [Jmol-users] smol files
On 6/30/2010 2:33 PM, Jeff Hansen wrote: Glad that helped. Making it easily accessible to students means doing most of the work for them. In the case of Jmol that means setting up buttons or checkboxes or whatever user interface then scripting what you want the students to see. In the case of viewing the MOs or some other surface you could create a button which the students would click to show the surface. Would be easy enough to include in that script a command to return to model 1 so the MOs would be available to view. Those surfaces in Spartan are basically the electron density surface colored according to other properties. Jmol will certainly allow you to visualize the electron density surface. My understanding is that you can also color it by whatever property you want. There would be some serious scripting involved in doing this. Without knowing exactly what is in the smol file, I would imagine the data for those properties are there somewhere. you would have to grab that data somehow then instruct Jmol to use it as the basis for coloring the surface. I'm no expert on this, but perhaps someone else can help with the details of this. Thanks for your suggestions. More or less that was my plan as far as buttons are concerned. I am trying to sort out what kind of files do I want to use as Jmol input, and what is the easiest way to set things up. I am at the exploratory stage (new to Jmol) so I running into occasional glitches as the one with vibrations/surface data. PM -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
I'm not having that problem at all with my Spartan files. I look at a vibration: frame 3; vibration on then go back to frame 1 and check the MO: frame 1; MO HOMO Works fine. Certainly Jmol is never no longer able to access Frame 1. Maybe you are just not going back to frame 1? On Wed, Jun 30, 2010 at 9:27 AM, Pshemak Maslak p...@chem.psu.edu wrote: On 6/30/2010 9:32 AM, Robert Hanson wrote:Coming back to my related questions: Can any other surfaces (in addition to MOs and mep) be visualized through smol files? vdw surface mapped with MEP is the most common: isosurface vdw map mep very pretty! And the MEP itself can be visualized, but that's not a common visualization. isosurface mep Can Jmol write jvxl files with multiple surfaces (for example selected MOs)? sure -- just make one JVXL file for each MO. This can be done with a pretty simple script if you needed to. The JVXL format does allow for multiple orbitals, but I haven't implemented that. Actaully, I think at one point Jmol could output every MO, but that takes so long and the file is so big, so I think that didn't make it into the release version of Jmol. I have a Spartan question: How do you construct an energy profile plot that allows you to easily correlate specific conformations to specific energies (as for example with butane)? I can do that in Sygress/CaCHE or using Spartan files with my Jmol/Google plot page, but is there some way of doing that directly in Spartan? Bob Thanks for all your help. PM On Wed, Jun 30, 2010 at 6:19 AM, Pshemak Maslak p...@chem.psu.edu wrote: On 6/29/2010 7:20 PM, Robert Hanson wrote: I'll look into the mep/mo business. Should not be a problem. Just a bug, I think. Thank you very much for your help. I do have two related questions: 1. Can more than one surface be read from these files by Jmol? 2. Can Jmol write jvxl files with multiple surfaces? Since I have just started learning Jmol and have noticed the incredible amount of work you have put into this project, I would like to take this opportunity to express my thanks for your contribution to the development of such an invaluable tool for organic chemists. PM On Mon, Jun 28, 2010 at 7:45 AM, Pshemak Maslak p...@chem.psu.edu wrote: On 6/25/2010 4:51 PM, Greeves, Nick wrote: I have used smol files for vibration e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well without any server side settings. All the best Nick Sent from my iPad Thank you very much for the example. Your case indeed clarifies the behavior: vibration and surfaces (mep and MOs) appear to be mutually exclusive with smol files, and if you do not reload, you cannot access the surfaces. Try the following: start any of the vibrations. Now stop it (check the vibration check box twice). Now check if MO's are still in the menu and what kind mep loads (not the one form smol, but one generated by Jmol). This is exactly what I was trying to explain (I am new to Jmol). That issue was not related to the MIME type question (although both were about smol). The same happens on the desktop Jmol. Thank you for your assistance. PM -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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 -- -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first -- ___ Jmol-users mailing listjmol-us...@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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
Re: [Jmol-users] smol files
I'll look into the mep/mo business. Should not be a problem. Just a bug, I think. On Mon, Jun 28, 2010 at 7:45 AM, Pshemak Maslak p...@chem.psu.edu wrote: On 6/25/2010 4:51 PM, Greeves, Nick wrote: I have used smol files for vibration e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well without any server side settings. All the best Nick Sent from my iPad Thank you very much for the example. Your case indeed clarifies the behavior: vibration and surfaces (mep and MOs) appear to be mutually exclusive with smol files, and if you do not reload, you cannot access the surfaces. Try the following: start any of the vibrations. Now stop it (check the vibration check box twice). Now check if MO's are still in the menu and what kind mep loads (not the one form smol, but one generated by Jmol). This is exactly what I was trying to explain (I am new to Jmol). That issue was not related to the MIME type question (although both were about smol). The same happens on the desktop Jmol. Thank you for your assistance. PM -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
On 6/25/2010 4:51 PM, Greeves, Nick wrote: I have used smol files for vibration e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well without any server side settings. All the best Nick Sent from my iPad Thank you very much for the example. Your case indeed clarifies the behavior: vibration and surfaces (mep and MOs) appear to be mutually exclusive with smol files, and if you do not reload, you cannot access the surfaces. Try the following: start any of the vibrations. Now stop it (check the vibration check box twice). Now check if MO's are still in the menu and what kind mep loads (not the one form smol, but one generated by Jmol). This is exactly what I was trying to explain (I am new to Jmol). That issue was not related to the MIME type question (although both were about smol). The same happens on the desktop Jmol. Thank you for your assistance. PM -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
As a workaround, you might load the file twice, and maybe that way you can use one for the vibrations, the other for the surface. load files myfile.smol myfile.smol -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
Hello, PM I am a new Jmol user and would like to learn more about smol files (Spartan, Wavefuction) Maybe this is not the best place to ask. You should address some Spartan community. 1. What is the MIME type for smol files to be correctly read on a server? As far as Jmol is concerned, file extensions and MIME types are irrelevant. Jmol will read the files and interpret their format irrespective of those issues. a) how can one read different surfaces outside of MOs and mep)? b) it appears that vibrational data can be read but they cannot be turned off, and once read they make surface data unavailable (and vice versa).Is there a solution to this issue? I cannot offer help on these, it depends on how the file reader parses the data. But do you mean when the file data is read by Jmol? Maybe you can look at the sample data files at http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/spartan/ those should be read correctly by Jmol. -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
On 6/25/2010 1:35 PM, Angel Herráez wrote: Hello, PM I am a new Jmol user and would like to learn more about smol files (Spartan, Wavefuction) Maybe this is not the best place to ask. You should address some Spartan community Thank you for your suggestion. Obviously, I would like to learn how smol files are read by Jmol (not what they are). 1. What is the MIME type for smol files to be correctly read on a server? As far as Jmol is concerned, file extensions and MIME types are irrelevant. Jmol will read the files and interpret their format irrespective of those issues. It is probably true on a desktop, but I do not think this is correct on a server. If a MIME type is not set, a file like.smol (or even jvxl) will not be read by the web app. My server can only read smol files after smol MIME was set to a generic application/octet-stream. Surprisingly Spartan technical help refers me to Jmol community for smol MIME type info. a) how can one read different surfaces outside of MOs and mep)? b) it appears that vibrational data can be read but they cannot be turned off, and once read they make surface data unavailable (and vice versa).Is there a solution to this issue? I cannot offer help on these, it depends on how the file reader parses the data. But do you mean when the file data is read by Jmol? Of course, I am referring to the reading of the file by Jmol. Maybe you can look at the sample data files at http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/spartan/ those should be read correctly by Jmol. Lmol will read correctly smol file with surface (or MO) data. I am referring to a situation where smol also contains vibrational frequency data. Reading of these does not work properly or at least interferes with reading of surface data. Your help is appreciated, PM -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
Hi again It is probably true on a desktop, but I do not think this is correct on a server. If a MIME type is not set, a file like.smol (or even jvxl) will not be read by the web app. I'm quite sure of this: Jmol does not care about MIME type. It may be that your server serves the files in a different way depending on their type, but I've never seen such a problem with Jmol. Remember that the web page does not link to or request the file, it is Jmol who does. I've used free (restricted) servers that don't allow me to upload a certain file type based on their extension, but MIME or Jmol have nothing to do there. By the way, try renaming the file e.g. to molecule.smol.txt. I've used that trick successfully with pdb files. Also, consider that Jmol reads both plian text files (like mol or pdb) and binary files (e.g. gzipped files) Are smol files binary?. My server can only read smol files after smol MIME was set to a generic application/octet- stream. Do yu have a url for your test page? How is the file being requested from the server? Never seen that. Surprisingly Spartan technical help refers me to Jmol community for smol MIME type info. Well, that's really FUNNY! Sorry I cannot help with the details of file parsing (when vibration and surfaces are there). Bob Hanson is your man for that; wait for his reply (or investigate the file reader yourself http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/adapter/readers/quantum/ -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] smol files
On 6/25/2010 2:42 PM, Angel Herráez wrote: It is probably true on a desktop, but I do not think this is correct on a server. If a MIME type is not set, a file like.smol (or even jvxl) will not be read by the web app. I'm quite sure of this: Jmol does not care about MIME type. It may be that your server serves the files in a different way depending on their type, but I've never seen such a problem with Jmol. Remember that the web page does not link to or request the file, it is Jmol who does. I've used free (restricted) servers that don't allow me to upload a certain file type based on their extension, but MIME or Jmol have nothing to do there. By the way, try renaming the file e.g. to molecule.smol.txt. I've used that trick successfully with pdb files. Also, consider that Jmol reads both plian text files (like mol or pdb) and binary files (e.g. gzipped files) Are smol files binary?. For Jmol it may not matter what the file is, but somehow the server does not know (without file extension association) that a file (smol or even jvxl) should be served to Jmol. Since the association asks for MIME type, I thought I have it set correctly. I was hoping somebody would know the true MIME for smol. [...] Sorry I cannot help with the details of file parsing (when vibration and surfaces are there). Bob Hanson is your man for that; wait for his reply (or investigate the file reader yourself http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/adapter/readers/quantum/ I have just started using Jmol and my plan was to be only the end-user. I will keep my fingers crossed and hope that somebody will be able to provide more guidance on smol files with multiple surfaces and vibrations. Thank you for all your help! PM -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] SMOL Files
Otis, I have no experience at all with Spartan, but as far as I reckon, smol is Spartan mol. You have several sample files at http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/spartan/ maybe the contents of some of them give you a clue Not really the same, but the MOL2 format (original from Sybyl) stores partial charges, and Jmol can buld the MEP from them. - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] SMOL Files
Otis, There are a few different Spartan file types, including .smol, .spartan, .sparchive, and full spardir Spartan directories that are zipped up (or not). Jmol recognizes them all. So save your file in whatever Spartan format you can, and see if Jmol will read it. If it doesn't, send the file to me. Bob Hanson Otis Rothenberger wrote: Hello- I'm interested in taking a closer look at using Jmol to display MEPS. The Jmol sample smol files for benzene and fluoromethane work very nicely. The smol file type appears to be a Spartan related file type. I'm having trouble tracking down information on this file type. Using Mac Spartan 06, there does not seem to be any smol option, nor does the Mac Spartan documentation reference this file type. Can anyone point me to more information about creating this file type from Spartan? Alternatively, are there any other suggestions regarding software packages, including Spartan, that can export Jmol readable files with electrostatic data for MEPS display? Otis Rothenberger [EMAIL PROTECTED] - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ 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 Northfield, MN http://www.stolaf.edu/people/hansonr 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 - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] SMOL Files
Bob and Angel, Thanks for the responses. My original thinking was that there was no way that Jmol was going to read the huge .spartan file for methane. Per Bob's note and Angel's note, wrong! It reads the file just fine. The resulting Jmol rendering of methane has vibration information, but not the electrostatic information for MEPS. We'll go back and do it again. I assume that we're not selecting the correct calculations in Spartan. I'll post a follow-up after we check this just to record a resolution to an issue that may be of interest to other users. Otis Bob Hanson wrote: Otis, There are a few different Spartan file types, including .smol, .spartan, .sparchive, and full spardir Spartan directories that are zipped up (or not). Jmol recognizes them all. So save your file in whatever Spartan format you can, and see if Jmol will read it. If it doesn't, send the file to me. Bob Hanson Otis Rothenberger wrote: Hello- I'm interested in taking a closer look at using Jmol to display MEPS. The Jmol sample smol files for benzene and fluoromethane work very nicely. The smol file type appears to be a Spartan related file type. I'm having trouble tracking down information on this file type. Using Mac Spartan 06, there does not seem to be any smol option, nor does the Mac Spartan documentation reference this file type. Can anyone point me to more information about creating this file type from Spartan? Alternatively, are there any other suggestions regarding software packages, including Spartan, that can export Jmol readable files with electrostatic data for MEPS display? Otis Rothenberger [EMAIL PROTECTED] - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] SMOL Files
Otis, Make sure under surfaces (in Spartan) you check potential. The Smol file will then work fine. You can check out a (rudimentary) example here: http://faculty.trinityvalleyschool.org/pricep/jmol/molimages/water.html Paul - Paul D. Price Science Dept. Chair Trinity Valley School Ft. Worth, Texas 76132 [EMAIL PROTECTED] From: Otis Rothenberger [EMAIL PROTECTED] Organization: CheMagic Reply-To: jmol-users@lists.sourceforge.net Date: Sun, 04 May 2008 21:36:56 -0500 To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] SMOL Files Bob and Angel, Thanks for the responses. My original thinking was that there was no way that Jmol was going to read the huge .spartan file for methane. Per Bob's note and Angel's note, wrong! It reads the file just fine. The resulting Jmol rendering of methane has vibration information, but not the electrostatic information for MEPS. We'll go back and do it again. I assume that we're not selecting the correct calculations in Spartan. I'll post a follow-up after we check this just to record a resolution to an issue that may be of interest to other users. Otis Bob Hanson wrote: Otis, There are a few different Spartan file types, including .smol, .spartan, .sparchive, and full spardir Spartan directories that are zipped up (or not). Jmol recognizes them all. So save your file in whatever Spartan format you can, and see if Jmol will read it. If it doesn't, send the file to me. Bob Hanson Otis Rothenberger wrote: Hello- I'm interested in taking a closer look at using Jmol to display MEPS. The Jmol sample smol files for benzene and fluoromethane work very nicely. The smol file type appears to be a Spartan related file type. I'm having trouble tracking down information on this file type. Using Mac Spartan 06, there does not seem to be any smol option, nor does the Mac Spartan documentation reference this file type. Can anyone point me to more information about creating this file type from Spartan? Alternatively, are there any other suggestions regarding software packages, including Spartan, that can export Jmol readable files with electrostatic data for MEPS display? Otis Rothenberger [EMAIL PROTECTED] - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaon e ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javao ne ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
