Re: [Jmol-users] rocketBarrels and arrows head
Hi Jaime 'set rocketBarrels' is working OK for me in 11.8.23, 11.8.24, 12.0.RC11 and 12.0.RC15 In general, is there an option to remove arrow heads? (beta sheets, ...) I don't think so. But I see no reason to be able to remove arrowheads from alpha rockets and not from beta rockets. Could be done together in my opinion. -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] rocketBarrels and arrows head
According to Angel Herráez angel.herr...@uah.es: 'set rocketBarrels' is working OK for me in 11.8.23, 11.8.24, 12.0.RC11 and 12.0.RC15 Thanks a lot. Will try again. Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] need 2-propenyl sulfenic acid molecular model
My son is doing a report on 2-propenyl sulfenic acid for his high school chemistry class. He would like to incorporate Jmol into his presentation ... and I think that is a good idea :) Q: Where can I get a file for 2-propenyl sulfenic acid? Thanks! Miguel -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
Hi Miguel! You can draw it and have Jmol optimize 3D Or draw it elsewhere and optimize 3D (I use ChemSketch) then save and open in Jmol -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
Coolest method: 1. find the SMILES string for 2-propenyl sulfenic acid 2. get the latest Jmol 12.0.RC 3. open the script console 4. type load $C=CCSO 5. watch the 3D structure appear in Jmol Kudos to Bob! -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
Hello, you could also try to search it on the net, maybe in this site http://cdb.ics.uci.edu/cgibin/ChemicalSearchWeb.psp regards -Ursprüngliche Nachricht- Von: Miguel Howard [mailto:mig...@jmol.org] Gesendet: Montag, 31. Mai 2010 18:16 An: jmol-users@lists.sourceforge.net Betreff: [Jmol-users] need 2-propenyl sulfenic acid molecular model My son is doing a report on 2-propenyl sulfenic acid for his high school chemistry class. He would like to incorporate Jmol into his presentation ... and I think that is a good idea :) Q: Where can I get a file for 2-propenyl sulfenic acid? Thanks! Miguel -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
Hello Miguel, I have Bob's IU server page discovery hooked to an unsigned applet via our server at chemagic. The following link should take you directly to the model your son needs: http://chemagic.com/web_molecules/script_page_large.aspx?smiles=C=CCSO Otis On 5/31/2010 2:01 PM, Angel Herráez wrote: Coolest method: 1. find the SMILES string for 2-propenyl sulfenic acid 2. get the latest Jmol 12.0.RC 3. open the script console 4. type load $C=CCSO 5. watch the 3D structure appear in Jmol Kudos to Bob! -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
Bob, the SMILES support is really *fantastic*! In the conversion from SMILES - 3D ... Q: ... are the atom locations more-or-less correct for a low-energy configuration? Q: ... are the bond angles more-or-less correct? Miguel -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] rocketBarrels and arrows head
I'm happy to remove arrow heads from the boxes with set rocketbarrels true Is it a common view to have no arrow heads at all? What does Pymol do? Bob On Mon, May 31, 2010 at 10:38 AM, jaime.prilu...@weizmann.ac.il wrote: According to Angel Herráez angel.herr...@uah.es: 'set rocketBarrels' is working OK for me in 11.8.23, 11.8.24, 12.0.RC11 and 12.0.RC15 Thanks a lot. Will try again. Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] set defaults pymol
Would it be reasonable to have a setting set defaults Pymol that matches settings in Pymol\? For example, perhaps something that would make the cartoons come up virtually identically to the way they appear in Pymol, and have antialiasDisplay on? Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
Otis, I had to load that page twice to have it work. Don't know why... Bob On Mon, May 31, 2010 at 1:09 PM, Otis Rothenberger osrot...@chemagic.comwrote: Hello Miguel, I have Bob's IU server page discovery hooked to an unsigned applet via our server at chemagic. The following link should take you directly to the model your son needs: http://chemagic.com/web_molecules/script_page_large.aspx?smiles=C=CCSO Otis On 5/31/2010 2:01 PM, Angel Herráez wrote: Coolest method: 1. find the SMILES string for 2-propenyl sulfenic acid 2. get the latest Jmol 12.0.RC 3. open the script console 4. type load $C=CCSO 5. watch the 3D structure appear in Jmol Kudos to Bob! -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
Bob, Right now I pass it from a server variable to a hidden field on the page load. This is followed by an onLoad call to a TimeOut() load into Jmol. I suspect that timing is the issue. I have to find a better way to do it. AJAX per your subsequent email may be the answer. If I understand AJAX, I will not have to do a new page load. I'm also having problems with triple bonds (#) in the query string. I guess I need to try sending escaped text. Otis On 5/31/2010 6:33 PM, Robert Hanson wrote: Otis, I had to load that page twice to have it work. Don't know why... Bob On Mon, May 31, 2010 at 1:09 PM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: Hello Miguel, I have Bob's IU server page discovery hooked to an unsigned applet via our server at chemagic. The following link should take you directly to the model your son needs: http://chemagic.com/web_molecules/script_page_large.aspx?smiles=C=CCSO Otis On 5/31/2010 2:01 PM, Angel Herráez wrote: Coolest method: 1. find the SMILES string for 2-propenyl sulfenic acid 2. get the latest Jmol 12.0.RC 3. open the script console 4. type load $C=CCSO 5. watch the 3D structure appear in Jmol Kudos to Bob! -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com http://chemagic.com -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] SMILES
Bob, Do you have any idea why this is returning propane and not 1-butyne? http://cheminfo.informatics.indiana.edu/rest/thread/d3.py/SMILES/CCC#C Otis On 5/31/2010 6:37 PM, Robert Hanson wrote: You could get it into a JavaScript variable using AJAX and then do anything you want with it. Bob On Sun, May 30, 2010 at 9:03 AM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: Bob, Following your note on SMILES (very nice addition by the way), I've been playing around with the Indiana University site. Since I have sever side programming control, I had no problem reading the IU http into a hidden field with subsequent load into the unsigned Jmol applet. I have to do this (the load) with JavaScript, however, and I was wondering about a direct load to Jmol. The IU return string (molfile) uses line-feeds. Below is their return for propane with bars replacing line-feeds. Is there any way to doctor this string so that Jmol will read it on a new load? I could write the unaltered file it to a temp file on the server and then load that as a molfile, but I'm curious about the possibility of reading the http stream into Jmol from my server directly on a fresh load. The UI file for propane with aforementioned line-feed swap: | PCMODEL v9.1 1.0 0.0|| 11 10 0 0 0 0 1 V2000| 1.3793 0.6283 0.5851 C 0 0 0 0 0 0 | 2.1939 1.8713 0.9005 C 0 0 0 0 0 0 | 2.4846 1.9884 2.3871 C 0 0 0 0 0 0 | 1.9120 -0.2779 0.8908 H 0 0 0 0 0 0 | 0.4143 0.6503 1.1018 H 0 0 0 0 0 0 | 1.1875 0.5634 -0.4904 H 0 0 0 0 0 0 | 1.6488 2.7601 0.5641 H 0 0 0 0 0 0 | 3.1383 1.8388 0.3457 H 0 0 0 0 0 0 | 1.5564 2.0516 2.9643 H 0 0 0 0 0 0 | 3.0724 2.8892 2.5888 H 0 0 0 0 0 0 | 3.0534 1.1241 2.7448 H 0 0 0 0 0 0 | 1 2 1 0| 1 4 1 0| 1 5 1 0| 1 6 1 0| 2 3 1 0| 2 7 1 0| 2 8 1 0| 3 9 1 0| 3 10 1 0| 3 11 1 0|M END| |-4.897042||| Otis -- Otis Rothenberger chemagic.com http://chemagic.com -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] SMILES
Bob, OK, I got it: 1. The url has to be encoded. 2. Which I tried before I wrote using ASP.NET UrlEncode 3) Hand entry of CCC%23C below works. 4) ASP.NET must be choking on # with Server.UrlEncode() Otis On 5/31/2010 9:14 PM, Otis Rothenberger wrote: Bob, Do you have any idea why this is returning propane and not 1-butyne? http://cheminfo.informatics.indiana.edu/rest/thread/d3.py/SMILES/CCC#C Otis On 5/31/2010 6:37 PM, Robert Hanson wrote: You could get it into a JavaScript variable using AJAX and then do anything you want with it. Bob On Sun, May 30, 2010 at 9:03 AM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: Bob, Following your note on SMILES (very nice addition by the way), I've been playing around with the Indiana University site. Since I have sever side programming control, I had no problem reading the IU http into a hidden field with subsequent load into the unsigned Jmol applet. I have to do this (the load) with JavaScript, however, and I was wondering about a direct load to Jmol. The IU return string (molfile) uses line-feeds. Below is their return for propane with bars replacing line-feeds. Is there any way to doctor this string so that Jmol will read it on a new load? I could write the unaltered file it to a temp file on the server and then load that as a molfile, but I'm curious about the possibility of reading the http stream into Jmol from my server directly on a fresh load. The UI file for propane with aforementioned line-feed swap: | PCMODEL v9.1 1.0 0.0|| 11 10 0 0 0 0 1 V2000| 1.3793 0.6283 0.5851 C 0 0 0 0 0 0 | 2.1939 1.8713 0.9005 C 0 0 0 0 0 0 | 2.4846 1.9884 2.3871 C 0 0 0 0 0 0 | 1.9120 -0.2779 0.8908 H 0 0 0 0 0 0 | 0.4143 0.6503 1.1018 H 0 0 0 0 0 0 | 1.1875 0.5634 -0.4904 H 0 0 0 0 0 0 | 1.6488 2.7601 0.5641 H 0 0 0 0 0 0 | 3.1383 1.8388 0.3457 H 0 0 0 0 0 0 | 1.5564 2.0516 2.9643 H 0 0 0 0 0 0 | 3.0724 2.8892 2.5888 H 0 0 0 0 0 0 | 3.0534 1.1241 2.7448 H 0 0 0 0 0 0 | 1 2 1 0| 1 4 1 0| 1 5 1 0| 1 6 1 0| 2 3 1 0| 2 7 1 0| 2 8 1 0| 3 9 1 0| 3 10 1 0| 3 11 1 0|M END| |-4.897042||| Otis -- Otis Rothenberger chemagic.com http://chemagic.com -- ___ 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Otis Rothenberger chemagic.com -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] rocketBarrels and arrows head
According to Robert Hanson hans...@stolaf.edu: I'm happy to remove arrow heads from the boxes with set rocketbarrels true It seems that this only works on alpha helices, no effect on beta sheets. Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Water related questions
Hi, Two water related questions: Is there an option for drawing water as crosses instead of spheres? Is there an option to 'set autobond OFF' only for water? Thanks, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
