Re: [Jmol-users] silica nanoparticle
On Fri, Jun 20, 2014 at 12:46 PM, Angel Herráez wrote: > My concerns are about correct atom position, and also adding more > atoms that were not present and should go in the right positions too. Understood and agreed... if I think of the nanotox field, however, they typically do not know how much, where, etc, the coating is covering the core... and I am under the impression it is actually the idea here to try to find some distribution to match experimental data... > For example, you could easily change all O atoms at a certain > distance from Si atoms and bonded in a certain way, into S atoms. But > then the bond lengths will not be correct, and how to add another > layer of atoms bonded to those S? Good questions, indeed. People have started doing QM-like things on this; for obvious reasons with methods like DFT etc. But you still have to start with some 3D model, and if this can be done with Jmol, it sounds like a win to me... Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: -0001-7542-0286 -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] silica nanoparticle
@Egon, > would it be very difficult to update the Jmol scripting language to > change the chemical nature (or just add atoms) to a selection of > atoms? > > That is, for spheric nanomaterials, one can probably select all atoms > at the surface (e.g. at a certain distance from the center of the > particle)... and then modify those atoms... > > Should be doable, right? Yes, I think it can be done easily, without any expnasion in the scripting language. My concerns are about correct atom position, and also adding more atoms that were not present and should go in the right positions too. For example, you could easily change all O atoms at a certain distance from Si atoms and bonded in a certain way, into S atoms. But then the bond lengths will not be correct, and how to add another layer of atoms bonded to those S? -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] silica nanoparticle
Kazem, On Fri, Jun 20, 2014 at 8:37 AM, Kazem Sepehrinia wrote: > I have made a silica nanoparticle using Materials Studio and I want to > modify surface chemistry of it, I want to remove unwanted groups from the > surface and create some new groups on the surface of nanoparticle in manner > that matches with experimental data. Do you have a file people can play with? As said in another reply, I guess with some scripting it should be doable... Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: -0001-7542-0286 -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] silica nanoparticle
Bob, On Fri, Jun 20, 2014 at 9:31 AM, Angel Herráez wrote: > I do not think that Jmol is your best tool for that, since I am > guessing there will be a lot of (repetitive) silica groups to which > the new groups must be added. Removal of groups is probably easy. > For just one addition it could be done, although still not the best > choice. would it be very difficult to update the Jmol scripting language to change the chemical nature (or just add atoms) to a selection of atoms? That is, for spheric nanomaterials, one can probably select all atoms at the surface (e.g. at a certain distance from the center of the particle)... and then modify those atoms... Should be doable, right? Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: -0001-7542-0286 -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] silica nanoparticle
Dear Angel Thanks for your consideration and quick response :-) Regards On Fri, Jun 20, 2014 at 12:01 PM, Angel Herráez wrote: > Hello Kazem > > I do not think that Jmol is your best tool for that, since I am > guessing there will be a lot of (repetitive) silica groups to which > the new groups must be added. Removal of groups is probably easy. > For just one addition it could be done, although still not the best > choice. > Although Jmol has some editing capabilities now, its design is of a > viewer, so building models is harder. An exception is the Model Kit > application like e.g. in Chemagic.com - but that's for single, small, > molecules and so far from your needs I think. > · > Dr. Angel Herráez > Biochemistry and Molecular Biology, > Dept. of Systems Biology, University of Alcalá > E-28871 Alcalá de Henares (Madrid), Spain > > > > -- > HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions > Find What Matters Most in Your Big Data with HPCC Systems > Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. > Leverages Graph Analysis for Fast Processing & Easy Data Exploration > http://p.sf.net/sfu/hpccsystems > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] silica nanoparticle
Hello Kazem I do not think that Jmol is your best tool for that, since I am guessing there will be a lot of (repetitive) silica groups to which the new groups must be added. Removal of groups is probably easy. For just one addition it could be done, although still not the best choice. Although Jmol has some editing capabilities now, its design is of a viewer, so building models is harder. An exception is the Model Kit application like e.g. in Chemagic.com - but that's for single, small, molecules and so far from your needs I think. · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] silica nanoparticle
Interesting use case! Egon http://enanomapper.net/ On Fri, Jun 20, 2014 at 8:37 AM, Kazem Sepehrinia wrote: > Hi, > > I have made a silica nanoparticle using Materials Studio and I want to > modify surface chemistry of it, I want to remove unwanted groups from the > surface and create some new groups on the surface of nanoparticle in manner > that matches with experimental data. > Can I do that using Jmol? Do you have a better suggestion for me? > > Regards, > Kazem Sepehrinia > > -- > HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions > Find What Matters Most in Your Big Data with HPCC Systems > Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. > Leverages Graph Analysis for Fast Processing & Easy Data Exploration > http://p.sf.net/sfu/hpccsystems > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: -0001-7542-0286 -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] silica nanoparticle
Hi, I have made a silica nanoparticle using Materials Studio and I want to modify surface chemistry of it, I want to remove unwanted groups from the surface and create some new groups on the surface of nanoparticle in manner that matches with experimental data. Can I do that using Jmol? Do you have a better suggestion for me? Regards, Kazem Sepehrinia -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
