Re: [Jmol-users] XYZ files with unit cell
Check the LOAD command docs. Jmol can add a unit cell to any file input. And add symmetry operation is desired. Very simple with xyz files. Your cored need to be Cartesian. Jmol will transform those into fractional coord prior to applying symmetry. Sent from my stupid iPhone On Nov 4, 2013, at 2:07 PM, Kurt Fredrickson wrote: > Hi there, > > I just started using Jmol a week ago, and it is very useful to see > vibrations! Right now I am inputting everything with an XYZ file. Is there > any way to add a rhombohedral unit cell frame to the vibration animations? > Right now, for my crystal I just have my atoms floating in space. > > captainalright > -- > November Webinars for C, C++, Fortran Developers > Accelerate application performance with scalable programming models. Explore > techniques for threading, error checking, porting, and tuning. Get the most > from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] XYZ files with unit cell
Hi Kurt I don't think that XYZ format supports crystallographic parameters.- You'd probably use another file format like CIF, more suited to inlcude that information. Otherwise, you can draw your "unitcell" from the coordinates, using the "draw" command -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] XYZ files with unit cell
Hi there, I just started using Jmol a week ago, and it is very useful to see vibrations! Right now I am inputting everything with an XYZ file. Is there any way to add a rhombohedral unit cell frame to the vibration animations? Right now, for my crystal I just have my atoms floating in space. captainalright -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Parsing JME string
Right you are on PubChem. When I look at the sdf for glucose, it's loaded with coordinate files! The 13.3.9 thing is real, however. Version 13.3.9 loads no double bond for a C=C SMILES query to Resolver. Version 13.3.3 gets it right. Same for name query. Carvone is OK with 13.3.3 - not so with 13.3.9. Since I'm working with a version link that Bob sent, I guess I should be more specific: 13.3.9_dev_20113.11.02 Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Nov 4, 2013, at 3:03 PM, Angel Herráez wrote: >> 3) PubChem loads are erratically funky. I got several glucose models loaded >> by one glucose >> query. This could be PubChem. I'll check it out/ > > Otis, my experience is that PubChem returns a multimodel sdf when it has > several hits for a name. Sometimes they are equivalent, other times they are > variants --like different ionization states of an amino acid. > > Check JSmol popup to see if there are more than 1 frames > > >> 4) http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm appears broken on >> Safari and Chrome. > > My Chrome Win7 fails to display the JSME object > (I think I saw it working yesterday) > and reports an alert > "The global function jsmeOnLoad is not defined or there might be a syntax > error in your javascript code" > > > > -- > Android is increasing in popularity, but the open development platform that > developers love is also attractive to malware creators. Download this white > paper to learn more about secure code signing practices that can help keep > Android apps secure. > http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Parsing JME string
> > 4) http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm appears broken on > > Safari and Chrome. Also broken in Firefox. The problem is the page is looking for JS/JSmolJME.js and the file exists in lowercase js/JSmolJME.js -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Parsing JME string
> 3) PubChem loads are erratically funky. I got several glucose models loaded > by one glucose > query. This could be PubChem. I'll check it out/ Otis, my experience is that PubChem returns a multimodel sdf when it has several hits for a name. Sometimes they are equivalent, other times they are variants --like different ionization states of an amino acid. Check JSmol popup to see if there are more than 1 frames > 4) http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm appears broken on > Safari and Chrome. My Chrome Win7 fails to display the JSME object (I think I saw it working yesterday) and reports an alert "The global function jsmeOnLoad is not defined or there might be a syntax error in your javascript code" -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Parsing JME string
I observe the same for item 4, with the following error: Warning: global function “jsmeOnLoad” is not defined. If you have defined it, there might be a syntax error in your javascript code. On Nov 4, 2013, at 2:15 PM, Otis Rothenberger wrote: > > 4) http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm appears broken on > Safari and Chrome. > > Otis > > > -- > Otis Rothenberger > o...@chemagic.com > http://chemagic.com > > > > > On Nov 4, 2013, at 12:19 PM, Robert Hanson wrote: > >> Jmol's minimization from SMILES is actually very very good -- it does not do >> this itself; instead, it sends it to CACTVS. If there is any delay, it is in >> that call. >> >> It's essential that you use >> >> autoez >> >> as one of the options to JME. JSmol adds that automaticallly. Please try a >> few of your molecules at >> >> http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm >> >> and tell me if there are any errors at all, and if so, send me enough >> information that I can reproduce the problem, if you can. >> >> I did see a problem there with 2D -> 3D not being converted properly when >> there is a "\" symbol in the SMILES string. That is fixed now on my site; >> files are at >> >> http://chemapps.stolaf.edu/jmol/jmol-13.3.9_2013.11.04.zip >> >> >> >> Bob >> >> >> >> On Sun, Nov 3, 2013 at 11:43 PM, 陈文瀚 wrote: >> load SMILES "xxx" is what I am using. However what I found it, the >> smiles string is not sufficient to depict the original 2D structure. >> Some of the molecules we tried to build lost the double bonds when we get >> the result from the cactus. That's why I am search for alternative >> solutions. So I am thinking of using the 2D representation of the structures >> e.g. the sdf file, but I was not able to foresee the conversion of the sdf >> file to other formats could be so troublesome. I thought it is >> straightforward in babel. However now I am stuck at the adding correct >> number of H atoms >> to the charged atoms in sdf file which is kind of disturbing. Anyway, I >> still am looking for ways to correct the number of H atoms. >> >> cheers, >> >> _ >> Wenhan Chen >> School of Chemistry and Molecular Biosciences >> The University of Queensland >> >> >> >> 2013/11/1 Robert Hanson >> The CACTVS server at NIH does a great job of turning 2D files into 3D. It's >> best not to have Jmol do that. You can pass the SMILES string from JME to >> Jmol; it will send it off to NIH. >> >> load SMILES "xxx" >> >> >> >> >> On Tue, Oct 29, 2013 at 7:55 PM, 陈文瀚 wrote: >> Actually if I transfer the structure from a mol file to JSmol and then try >> to optimize the structure, the charity cannot be preserved as well ... >> >> >> >> _ >> Wenhan Chen >> School of Chemistry and Molecular Biosciences >> The University of Queensland >> >> >> >> 2013/10/30 陈文瀚 >> Basically, molecules with more than 30 atoms sent in JME format(not >> including H) will cause a halt for the browser as the js try to hold the >> browser. >> But you are right, it was quick using Jmol with JRE. I think JSmol try to do >> EM using MMFF which takes the most time. >> When the molecule in MOL format passes onto JSmol, it works fine with no EM. >> >> Even so I still am trying to address the problem using mol format, as the >> charge information (the number of H atoms) in the mol file is not presented >> right in JSmol. >> >> Herein is an example : >> >>C+ >> / \ >> C -- -C >> The mol file for the above mol is : >> >> CWRITER31030r]09392D >> Created with ChemWriter - http://chemwriter.com >> 3 3 0 0 0 0 0 0 0 0999 V2000 >> >> 4.3530 -4.78300. C 0 0 0 0 0 0 0 0 0 0 0 0 >> 5.3530 -4.78300. C 0 0 0 0 0 0 0 0 0 0 0 0 >> 4.8530 -3.91690. C 0 0 0 0 0 0 0 0 0 0 0 0 >> 1 2 1 0 0 0 >> 2 3 1 0 0 0 >> 3 1 1 0 0 0 >> M CHG 1 3 1 >> M END >> >> JSmol cannot add an H atom to the C+ atom. >> >> >> >> >> _ >> Wenhan Chen >> School of Chemistry and Molecular Biosciences >> The University of Queensland >> >> >> >> 2013/10/30 Angel Herráez >> Thanks for the feedback, Pino >> >> Then maybe the 3D minimization is much slower in the Javascript >> version that in the Java version. >> >> I've now added an option to the JSME page to check if it is the >> transfer (unlikely), adding the hydrogens or the 3D minimization >> which gives the delay >> That is only useful for MOL transfer. >> JME transfer must necessarily go to 3D conversion, that may be the >> bottleneck. >> >> It seems indeed that it is the JmeReader routine that takes its time >> >> >> >> -- >> Android is increasing in popularity, but the open development platform that >
[Jmol-users] Super Simple JSMol
I have been out of the loop for a while taking care of my wife who has a broken and repaired knee cap. I knew we ought to pay off those gambling debts:-) I have been looking today at the Super Simple JSmol page (http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm). It works fine in Mavericks using Firefox 25 and on my iPhone (iOS7). However, the HTML5 link does not work in Safari. A new page is launched with the search bar, but the applet (or whatever we are now calling it) does not load even after waiting for 10 minutes. On the other hand, if I simply open the “Show Error Console” in the developers menu in Safari, the HTML5 loads fine. It is not clear to why simply having the console open allows jsmol to load. Is it a timing thing?? I see the following error messages in the console for the incident when jsmol did not load: [Error] Failed to load resource: the server responded with a status of 503 (Service Unavailable) (get-js, line 0) [Error] java.lang.NullPointerException (anonymous function) (core.z.js, line 398) (anonymous function) (core.z.js, line 2256) (anonymous function) (core.z.js, line 2248) (anonymous function) (core.z.js, line 2225) instantialize (JSmol.min.js, line 343) (anonymous function) (core.z.js, line 2223) innerTypeInstance (JSmol.min.js, line 358) (anonymous function) (core.z.js, line 2192) (anonymous function) (core.z.js, line 938) (anonymous function) (core.z.js, line 926) (anonymous function) (core.z.js, line 917) instantialize (JSmol.min.js, line 343) (anonymous function) (core.z.js, line 913) (anonymous function) (core.z.js, line 506) (anonymous function) (core.z.js, line 506) (anonymous function) (core.z.js, line 504) instantialize (JSmol.min.js, line 343) (anonymous function) (core.z.js, line 503) __startAppletJS (JSmol.min.js, line 256) __nextExecution (JSmol.min.js, line 261) Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Parsing JME string
I don't know if this is related to this thread, but several points: 1) I just noticed that 13.3.9 appears to be broken on an NCI load. Double bonds are missing on a name load and a SMILES load. 2) The above sdf's are OK, so I think is JSmol 3) PubChem loads are erratically funky. I got several glucose models loaded by one glucose query. This could be PubChem. I'll check it out/ 4) http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm appears broken on Safari and Chrome. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Nov 4, 2013, at 12:19 PM, Robert Hanson wrote: > Jmol's minimization from SMILES is actually very very good -- it does not do > this itself; instead, it sends it to CACTVS. If there is any delay, it is in > that call. > > It's essential that you use > > autoez > > as one of the options to JME. JSmol adds that automaticallly. Please try a > few of your molecules at > > http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm > > and tell me if there are any errors at all, and if so, send me enough > information that I can reproduce the problem, if you can. > > I did see a problem there with 2D -> 3D not being converted properly when > there is a "\" symbol in the SMILES string. That is fixed now on my site; > files are at > > http://chemapps.stolaf.edu/jmol/jmol-13.3.9_2013.11.04.zip > > > > Bob > > > > On Sun, Nov 3, 2013 at 11:43 PM, 陈文瀚 wrote: > load SMILES "xxx" is what I am using. However what I found it, the smiles > string is not sufficient to depict the original 2D structure. > Some of the molecules we tried to build lost the double bonds when we get the > result from the cactus. That's why I am search for alternative > solutions. So I am thinking of using the 2D representation of the structures > e.g. the sdf file, but I was not able to foresee the conversion of the sdf > file to other formats could be so troublesome. I thought it is > straightforward in babel. However now I am stuck at the adding correct number > of H atoms > to the charged atoms in sdf file which is kind of disturbing. Anyway, I still > am looking for ways to correct the number of H atoms. > > cheers, > > _ > Wenhan Chen > School of Chemistry and Molecular Biosciences > The University of Queensland > > > > 2013/11/1 Robert Hanson > The CACTVS server at NIH does a great job of turning 2D files into 3D. It's > best not to have Jmol do that. You can pass the SMILES string from JME to > Jmol; it will send it off to NIH. > > load SMILES "xxx" > > > > > On Tue, Oct 29, 2013 at 7:55 PM, 陈文瀚 wrote: > Actually if I transfer the structure from a mol file to JSmol and then try to > optimize the structure, the charity cannot be preserved as well ... > > > > _ > Wenhan Chen > School of Chemistry and Molecular Biosciences > The University of Queensland > > > > 2013/10/30 陈文瀚 > Basically, molecules with more than 30 atoms sent in JME format(not including > H) will cause a halt for the browser as the js try to hold the browser. > But you are right, it was quick using Jmol with JRE. I think JSmol try to do > EM using MMFF which takes the most time. > When the molecule in MOL format passes onto JSmol, it works fine with no EM. > > Even so I still am trying to address the problem using mol format, as the > charge information (the number of H atoms) in the mol file is not presented > right in JSmol. > > Herein is an example : > >C+ > / \ > C -- -C > The mol file for the above mol is : > > CWRITER31030r]09392D > Created with ChemWriter - http://chemwriter.com > 3 3 0 0 0 0 0 0 0 0999 V2000 > > 4.3530 -4.78300. C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.3530 -4.78300. C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.8530 -3.91690. C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 0 0 > 2 3 1 0 0 0 > 3 1 1 0 0 0 > M CHG 1 3 1 > M END > > JSmol cannot add an H atom to the C+ atom. > > > > > _ > Wenhan Chen > School of Chemistry and Molecular Biosciences > The University of Queensland > > > > 2013/10/30 Angel Herráez > Thanks for the feedback, Pino > > Then maybe the 3D minimization is much slower in the Javascript > version that in the Java version. > > I've now added an option to the JSME page to check if it is the > transfer (unlikely), adding the hydrogens or the 3D minimization > which gives the delay > That is only useful for MOL transfer. > JME transfer must necessarily go to 3D conversion, that may be the > bottleneck. > > It seems indeed that it is the JmeReader routine that takes its time > > > > -- > Android is increasing in popularity, but the open development platform that > developers love is also attractive to ma
Re: [Jmol-users] Fwd: test2.htm page
Hi Dave Yes, then it's going to be tricky. I have Firefox 24.0 on Win8, and the models are loading fine. I cleared cache, also entered other names in the slot. They work. Updated to Firefox 25. Working too > (using the full URL with the file format parameters). And the Jmol/Java > example works, so I guess the NIH server is OK. Yes, of course you are right on that. Sorry > But that Jmol/HTML5 > example page fails 100% in the same way. > I'm just trying to report what appears to be a problem. If there's some > way I can provide more information to help track it down, please let me > know. I don't see how we can track this down Chrome v 30.0 and IE10.0 work too · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] R: Re: Parsing JME string
Jmol's minimization from SMILES is actually very very good -- it does not do this itself; instead, it sends it to CACTVS. If there is any delay, it is in that call. It's essential that you use autoez as one of the options to JME. JSmol adds that automaticallly. Please try a few of your molecules at http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm and tell me if there are any errors at all, and if so, send me enough information that I can reproduce the problem, if you can. I did see a problem there with 2D -> 3D not being converted properly when there is a "\" symbol in the SMILES string. That is fixed now on my site; files are at http://chemapps.stolaf.edu/jmol/jmol-13.3.9_2013.11.04.zip Bob On Sun, Nov 3, 2013 at 11:43 PM, 陈文瀚 wrote: > load SMILES "xxx" is what I am using. However what I found it, the > smiles string is not sufficient to depict the original 2D structure. > Some of the molecules we tried to build lost the double bonds when we get > the result from the cactus. That's why I am search for alternative > solutions. So I am thinking of using the 2D representation of the > structures e.g. the sdf file, but I was not able to foresee the conversion > of the sdf > file to other formats could be so troublesome. I thought it is > straightforward in babel. However now I am stuck at the adding correct > number of H atoms > to the charged atoms in sdf file which is kind of disturbing. Anyway, I > still am looking for ways to correct the number of H atoms. > > cheers, > > _ > Wenhan Chen > School of Chemistry and Molecular Biosciences > The University of Queensland > > > > 2013/11/1 Robert Hanson > >> The CACTVS server at NIH does a great job of turning 2D files into 3D. >> It's best not to have Jmol do that. You can pass the SMILES string from JME >> to Jmol; it will send it off to NIH. >> >> load SMILES "xxx" >> >> >> >> >> On Tue, Oct 29, 2013 at 7:55 PM, 陈文瀚 wrote: >> >>> Actually if I transfer the structure from a mol file to JSmol and then >>> try to optimize the structure, the charity cannot be preserved as well ... >>> >>> >>> >>> _ >>> Wenhan Chen >>> School of Chemistry and Molecular Biosciences >>> The University of Queensland >>> >>> >>> >>> 2013/10/30 陈文瀚 >>> Basically, molecules with more than 30 atoms sent in JME format(not including H) will cause a halt for the browser as the js try to hold the browser. But you are right, it was quick using Jmol with JRE. I think JSmol try to do EM using MMFF which takes the most time. When the molecule in MOL format passes onto JSmol, it works fine with no EM. Even so I still am trying to address the problem using mol format, as the charge information (the number of H atoms) in the mol file is not presented right in JSmol. Herein is an example : C+ / \ C -- -C The mol file for the above mol is : CWRITER31030r]09392D Created with ChemWriter - http://chemwriter.com 3 3 0 0 0 0 0 0 0 0999 V2000 4.3530 -4.78300. C 0 0 0 0 0 0 0 0 0 0 0 0 5.3530 -4.78300. C 0 0 0 0 0 0 0 0 0 0 0 0 4.8530 -3.91690. C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 2 3 1 0 0 0 3 1 1 0 0 0 M CHG 1 3 1 M END JSmol cannot add an H atom to the C+ atom. _ Wenhan Chen School of Chemistry and Molecular Biosciences The University of Queensland 2013/10/30 Angel Herráez > Thanks for the feedback, Pino > > Then maybe the 3D minimization is much slower in the Javascript > version that in the Java version. > > I've now added an option to the JSME page to check if it is the > transfer (unlikely), adding the hydrogens or the 3D minimization > which gives the delay > That is only useful for MOL transfer. > JME transfer must necessarily go to 3D conversion, that may be the > bottleneck. > > It seems indeed that it is the JmeReader routine that takes its time > > > > > -- > Android is increasing in popularity, but the open development platform > that > developers love is also attractive to malware creators. Download this > white > paper to learn more about secure code signing practices that can help > keep > Android apps secure. > > http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > >>> >>> >>> ---
Re: [Jmol-users] Fwd: test2.htm page
Angel Herráez wrote: > It worked for me yesterday (and just now too) > I guess the NIH server is not working full-time good (still under > restrictions of FedGov, or is that solved?) If I request the data file directly from NIH, it comes without a problem (using the full URL with the file format parameters). And the Jmol/Java example works, so I guess the NIH server is OK. But that Jmol/HTML5 example page fails 100% in the same way. I'm just trying to report what appears to be a problem. If there's some way I can provide more information to help track it down, please let me know. FWIW, I'm using FF 25.0 on Ubuntu 12.04 Cheers, Dave > Dave Howorth wrote: >> When I go to that page, I see two buttons. >> If I click on the Jmol/Java one, I see a caffeine molecule. >> If I click on the Jmol/HTML5 one, I eventually see >> >> "unrecognized file format for file http://cactus.nci.nih.gov/chem";... > > > > -- > Android is increasing in popularity, but the open development platform that > developers love is also attractive to malware creators. Download this white > paper to learn more about secure code signing practices that can help keep > Android apps secure. > http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Fwd: test2.htm page
It worked for me yesterday (and just now too) I guess the NIH server is not working full-time good (still under restrictions of FedGov, or is that solved?) Dave Howorth wrote: > When I go to that page, I see two buttons. > If I click on the Jmol/Java one, I see a caffeine molecule. > If I click on the Jmol/HTML5 one, I eventually see > > "unrecognized file format for file http://cactus.nci.nih.gov/chem";... -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Fwd: test2.htm page
Robert Hanson wrote: > With jQuery, you can very easily set buttons to do this on the current page > without reloading the page. Here is an example: > > http://chemapps.stolaf.edu/jmol/jsmol/simpleOpt.htm When I go to that page, I see two buttons. If I click on the Jmol/Java one, I see a caffeine molecule. If I click on the Jmol/HTML5 one, I eventually see "unrecognized file format for file http://cactus.nci.nih.gov/chem";... > Bob -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] R: Re: Parsing JME string
Hello Wenhan Chen I see that the slow part is optimizing the 3D geometry from JME format, maybe from smiles too. See my updated page http://biomodel.uah.es/en/DIY/JSME/ Using the "diagnostics" you will see the difference. I think MOL format is the fastest. I have managed to solve the problem I had with tertiary carbons. About your specific problme with charged atoms, you will have to test which format is best understood. > load SMILES "xxx" is what I am using. However what I found it, > the smiles string is not sufficient to depict the original 2D > structure. Well, smiles is 1D, so there may be limitations. It works with normal structures,. but yours seem to be special. > Some of the molecules we tried to build lost the double bonds when we > get the result from the cactus. MOL will be better at keeping the double bonds. > conversion of the sdf > file to other formats could be so troublesome. I thought it is > straightforward in babel. That's what Babel is made for -- format conversions. You should not really need to convert formats, just use one that is best written by JSME and read by JSmol However now I am stuck at the adding > correct number of H atoms > to the charged atoms in sdf file which is kind of disturbing. Anyway, > I still am looking for ways to correct the number of H atoms. I've drawn this C+ / \ C -- -C and transferred as mol: I get cyclo CH2-CH2-CH and the +1 charge is there: label %[charge]; color label yellow; font label 22; Transfer as JME works too, and smiles too Not for you? -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] inline load combined with filter
El 31 Oct 2013 a las 14:37, Robert Hanson escribió: > all the filter business works with load inline and load DATA. Are you > finding it not working? Well, yes, I was getting syntax errors in the console when trying to use both inline and filter But I cannot reproduce now, it's working. Forget it, thanks -- Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
