Re: [Jmol-users] silica nanoparticle
Interesting use case! Egon http://enanomapper.net/ On Fri, Jun 20, 2014 at 8:37 AM, Kazem Sepehrinia ksepehri...@gmail.com 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
Re: [Jmol-users] silica nanoparticle
Bob, On Fri, Jun 20, 2014 at 9:31 AM, Angel Herráez angel.herr...@uah.es 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
Kazem, On Fri, Jun 20, 2014 at 8:37 AM, Kazem Sepehrinia ksepehri...@gmail.com 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
On Fri, Jun 20, 2014 at 12:46 PM, Angel Herráez angel.herr...@uah.es 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
[Jmol-users] CML for animations?
Hi all, the CDK has code to read CML files with a JMOL-ANIMATION convention which was one used to store Jmol animations in the Chemical Markup Language. Is anyone using this convention or using CML in general for conventions? 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 -- Subversion Kills Productivity. Get off Subversion Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] CML for animations?
On Thu, Mar 6, 2014 at 3:49 PM, Robert Hanson hans...@stolaf.edu wrote: What does that even mean, Jmol-Animation convention? convention is a concept from the Chemical Markup Language format. A convention refers to how various CML elements encode particular content. And how could you possibly save that in CML? More or less in the same way as in a XYZ file: a sequence of 3D models... 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 -- Subversion Kills Productivity. Get off Subversion Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] CML for animations?
On Thu, Mar 6, 2014 at 4:00 PM, Robert Hanson hans...@stolaf.edu wrote: sure. I see. Right. Standard, simple animation. Thank you. And your questions basically confirm my suspicion :) Thanks, 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 -- Subversion Kills Productivity. Get off Subversion Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] posterity link -- Jmol-7
On Wed, Apr 3, 2013 at 10:33 PM, Robert Hanson hans...@stolaf.edu wrote: Oh my! http://www.chm.bris.ac.uk/jmol/jmol-7/ Nice, but it does not beat Jmol 0.6 from March 2001: jmol-0.6.1.tar.gz 2001-03-26 2.9 MB - https://sourceforge.net/projects/jmol/files/OldFiles/ That said, there is not much around anymore showing early adoption :( Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.1.13 released - several new features
On Fri, Feb 22, 2013 at 5:59 PM, Robert Hanson hans...@stolaf.edu wrote: A lofty goal. No such plans at this stage. Understood, and no worries :) There will always be plenty of ideas, but without the bank account of someone like Gates or Slim, we won't be able to implement them all :) Plenty to do just to get the reading working. But I wouldn't rule it out. Yeah, we can keep dreaming :) The problem, of course, would be that a significant portion of what Jmol is capable of doing is not representable in PyMOL. And, I'm sure, vice-versa, but that's not stopping me from trying Indeed. I would personally not be so worried about that; there is a common basis and that could start really small and it would grow over time, as people coin in, add effort etc, just like with Jmol itself... to many efforts fail in that the measure success only in the best possible outcome that turned out to be too ambitious... like Rome, Jmol was not built in one day either. On a related note, I have written a patch (now applied) that splits the Jmol editor in Bioclipse, to have one for small molecules and one for large molecules. That will allow us to tune menu's etc for the various content. While I am full time working on Open PHACTS, I do teach a few hours of Protein Structure each year, and moving to Bioclipse/Jmol as platform for that. I am thinking of something like Proteopedia here, which I really like. I very briefly tried to upgrade Jmol in Bioclipse last week; Bioclipse 2.6.0 uses 11.8.17. I tried upgrading to 13.x but there were too many API changes. Is there an migration help page, by any change? And, would it already be worth upgrading to the latest 11.x? That would be easier and still perhaps improve Bioclipse 2.6.1 ? Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.1.13 released - several new features
On Fri, Feb 22, 2013 at 1:27 AM, Robert Hanson hans...@stolaf.edu wrote: Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is still work to be done to ensure faithful rendition, but it's a start. Nice! Do you also have in mind of writing such files? That would very nicely implement an idea that no one ever got around too, of sharing views between PyMOL and Jmol... Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and MMFF94
On Wed, May 16, 2012 at 11:00 PM, Robert Hanson hans...@stolaf.edu wrote: Thank you, Nico, for releasing Jmol 12.3.25. This version of Jmol is very special. It includes set forcefield MMFF Well done! Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bye Bye mmCIF?
On Sun, Apr 22, 2012 at 10:40 PM, Eric Martz ema...@microbio.umass.edu wrote: This is the first I've heard about PWF. There are some slides by Helen Berman about it here: http://www.rcsb.org/pdb/general_information/about_pdb/rcsbpdbac10-presentations.pdf Listening to a talk from Gerard Kleywegt (PDBe) right now, who just said the wwPDB is in fact based on mmCIF (with PDBx)... I asked about a draft specification, and he mentioned they are working on a website, but had no further detail... Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol/ChemDoodle -- test2
On Fri, Apr 13, 2012 at 7:03 AM, Robert Hanson hans...@stolaf.edu wrote: OK. Please test! http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm Very nice! Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] What's the status of Jmol and the IcedTea Plugin?
Hi Jonathan, On Fri, Mar 23, 2012 at 11:46 PM, Jonathan Gutow gu...@uwosh.edu wrote: This suggests that there is a workaround for getting Jmol to work with the IcedTea plugin. I thought from reading it that IcedTea couldn't handle the segmented loading. The applet loads for me nowadays in Chrome on Debian testing with the IcedTea plugin for applets and IcedTea/OpenJDK, but the when I try Proteopedia, clicking a green link causes the applet view to blank :( Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol for iPads?
On Thu, Mar 29, 2012 at 3:08 PM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote: 1. Do you want a QA controlled (by Apple) environment, or the more advertising-oriented environment of Android? I do have several Android apps installed without advertisement... I do not think the above choice is accurate... 2. Which app store best contains the kind of apps that you want? Here too, you have way more choice with Android: e.g. there is F-Droid, an app store dedicated to open source apps: http://f-droid.org/ (Bob, maybe you could upload the Jmol app there too?) 4. Security, again allegedly, is lower on Android. F-Droid has interesting apps in this area... 5. iPad is not fragmented, but Android is device fragmented (unless of course you consider Samsung as the only alternative player). Choice == fragmentation. Do you want a monopoly (no fragmentation) or a choice (fragmentation)... if you rather pay a lot for not having to make choices, then iPad is your thing. If you like to encourage your students to explore things no one has done before, then iPad/Android is even be a choice. 6. Few Android devices update the OS as often as Apple does IOS. Android's can be installed with custom ROMs which you can update any time of the day you like. Forcing your students to use certain hardware and certain software may sound cool, but ask a student and ask him/her why she cannot as study as optimal as he/she would like... you'll hear one thing: access to study material. So, if you go iPad, make sure that all students has iPads 24/7 and can install/view and study whatever educational material they deem needed... I find it very disturbing that educators are even considering creating a learning environment where students are restricted in their learning! That is just another step back to the middle ages... Henry, I very much appreciate that people use the platform on which they can perform their work most efficient; do not disallow your students the same choice! Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol for iPads?
Dear Henry, On Fri, Mar 30, 2012 at 11:01 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote: I find it very disturbing that educators are even considering creating a learning environment where students are restricted in their learning! That is just another step back to the middle ages... Henry, I very much appreciate that people use the platform on which they can perform their work most efficient; do not disallow your students the same choice! I a not sure I understand what you are saying Egon. If there is eg no Jmol on e.g. an iPad or Kindle, is that extending choice? It most certainly is not... I would love to see Jmol work on the iPad or Kindle... It could be viewed as a lack of choice, ie if you want the features of Jmol on a mobile device, your choice is currently restricted just to Android. 'just' :) I mentioned in my post standards, ie epub2, epub3. There are widely available readers for these on all platforms (well, not yet epub3, but it will come). Again, I am not sure where the lack of choice there is? I am wondering if these will allow the interactivity we want as done in Proteopedia. Will those formats be an electronic dead tree, or proper HTML with embedding of interactive things (applet/WebGL/...) which can be interacted with? WebGL is expected shortly on both types, again no lack of choice. My argument was not against WebGL, but against iPad, and in reply to your 8 points in comparing iPad to Android... The interaction and accessibility is crucial... we want students to not just look at a protein, but indeed also to allow them do things the material did not immediately envision, like the downloading of that structure into other tools... Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol for iPads?
All, On Fri, Mar 30, 2012 at 10:29 AM, Egon Willighagen egon.willigha...@gmail.com wrote: I find it very disturbing that educators are even considering creating a learning environment where students are restricted in their learning! That is just another step back to the middle ages... Henry, I very much appreciate that people use the platform on which they can perform their work most efficient; do not disallow your students the same choice! I like to clarify this point a bit. In was partly in reply to the email from Henry, but also to other emails in this thread. What I observe at many universities is plans where the university has beautiful plans how they like to teach students. This can be a choice for using iPad to show students protein structures, as outed in the email thread. We have seen this for a long time: we select one pedagogical book for a topic. However, that one book may not align best with how all students learn; probably it will with the majority, but not all. Maastricht University expects students to decide themselves which book to pick, and we here offer them two or three options. However, this has as downside that they can only read them at the university, as we do not provide those books for free, nor expect them to buy them (which they would not be able to, anyway). Here, the educational institute 'knows best' how the students will learn. However, all students have their own way of learning. Some prefer learning basic facts by heart, others prefer understanding and apply systems later. Similarly, there are various ways to explain something. Pure mathematics, visual explanation, explanation by example. Books prefer solutions. But who are we to decide what is best? Should we keep acting like a church that describes what is best for the flock? That is where my clumsy referral to the middle ages come from: an institute that decides what it best, leaving no option for alternatives. I should have phrased it like that. My apologies that the email reads like a flamebait; I am strong about teaching students to think for themselves, which requires giving them room to make choices for themselves; I was overenthusiastic about it. Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol for iPads?
On Thu, Mar 29, 2012 at 4:19 AM, Craig T Martin cmar...@chem.umass.edu wrote: I don't yet have an iPad personally, but it's on my list of things to buy next and I have a number of colleagues who are absolutely fanatical. Tomorrow we go to the Dean to pitch an idea that will involve the purchase of 200 iPads, for laboratory and evening exam use. The latter would benefit greatly from jmol adaptation. Anyone game to take this on? Bringing jmol out of Java and into HTML5/OpenGL? Why not pitch that idea you with Dean too then? Closed platforms do come with a more limited amount of software... why not ask for permission to purchase development time for someone to write this code transition? Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol for iPads?
On Fri, Mar 23, 2012 at 8:33 PM, Eric Martz ema...@microbio.umass.edu wrote: I just heard a segment on NPR about hundreds of high schools that are abandoning textbooks and giving every student an iPad instead. This is so sad... we're not even over the MS vendor lock-in, and ready to buy into the next one... Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol applet in HTML...
2012/1/29 Herráez Sánchez Ángel angel.herr...@uah.es: Everything you describe sounds like the regular and proper way to do. It may be your browser, but I would not expect it. Any modern browsers now behave, and Iceweasel is Gecko-based, right? Iceweasel is just Firefox, but the name 'firefox' is trademarked and not 'open', so Debian cannot use it. Hence 'iceweasel'. I would more expect the Java plugin to be a problem, which is icedtea... Both my Chrome and Iceweasel use that... I got Konqueror working now, which uses a java executable directly, rather than a Java plugin... while needlessly slow (takes 20 seconds to fire up), it does show be crambin and caffeine... so, there the file IO jars are properly loaded... Also, it works in Konqueror with both 12.2.0 and 12.2.13, while neither in Chrome and Icedweasel, so there does not seem to be regression in the indexing either... I will try to figure out if the single jar approach works, but need to figure out how to initialize that with Jmol.js... Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol applet in HTML...
2012/1/29 Herráez Sánchez Ángel angel.herr...@uah.es: I recollect other people reporting problems with IcedTea, may be that. ... jmolInitialize(.., JmolApplet.jar) Yeah, I'd found that too and using the signed full jar... and that works in Konqueror, Icedweasel, and Chrome. So, I think we isolated indeed the problem to the IcedTea plugin... and just to be clear, this plugin is using the same Java as Konqueror is using directly... and that is OpenJDK 6. OK, thanx for the help! I will be talking to the IcedTea community now, primarily to ask if this is a know issue yet... Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] running a localized Jmol application on OS/X? (was: Översättning igen)
cc:jmol-user Hi Peter, 2012/1/16 Peter Sahlin peter.sah...@akademi.bastad.se: Hope you can read my swedish, otherwise tell me and I will translate. Yeah, I could read it :) I'm not a native speaker, but in the past three years up picked it up a bit. Hämtade Jmol 12.3.12 igår, men där fick jag ingen svenska alls. Hämtade då Jmol 12.2.12 (har använt 12.0.45 förut) men här fungerade inte översättningen heller. Ändå gav menyn nere till höger valet Svenska. Jag bytte till brittisk engelska, och sedan tillbaka till svenska, men det hjälpte inte. Kollade sedan i javakonsolen och där stod: GT could not find the class org.jmol.translation.Jmol.en_GB.Messages_en_GB GT could not find the class org.jmol.translation.JmolApplet.en_GB.Messages_en_GB GT could not find the class org.jmol.translation.Jmol.sv.Messages_sv GT could not find the class org.jmol.translation.Jmol.sv.Messages_sv Har jag gjort något fel?? From the error messages I would say you have a .jar file missing, but I do not own a Mac myself, and do not know why it does not see the .jar with translations... Jmol user community, how should OS/X users start Jmol to get translations to work properly? Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- RSA(R) Conference 2012 Mar 27 - Feb 2 Save $400 by Jan. 27 Register now! http://p.sf.net/sfu/rsa-sfdev2dev2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol Android released
On Mon, Dec 5, 2011 at 2:49 PM, Robert Hanson hans...@stolaf.edu wrote: https://market.android.com/search?q=jmolso=1 Cool! And now that I actually have an android, even cooler! Q: is it possible to create a URL or so, that would auto load the app with a particular protein? Or better: with a particular Jmol script? What I am getting at, is that I want to have QR codes on slides on lectures, allowing students to open the structures I am displaying on the slide, directly on their phones... Egon -- Dr E.L. Willighagen Postdoctoral Researcher 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 -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please UNsubsribe me from the jmol users email list, thanks
Dear Clifford, On Tue, Dec 6, 2011 at 9:00 AM, Clifford Felder clifford.fel...@weizmann.ac.il wrote: Please UNsubsribe me from the jmol users email list, thanks Sincerely, Clifford (Chaim Tzvi) Felder clifford.fel...@weizmann.ac.il You can do this yourself by going to this webpage: https://lists.sourceforge.net/lists/listinfo/jmol-users Scroll down the bottom, enter your subscribed email address and click the Unsubscribe button. With kind regards, Egon Willighagen -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) 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 -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] interesting factoid -- Jmol in Google Documents
On Tue, Nov 22, 2011 at 3:41 AM, Robert Hanson hans...@stolaf.edu wrote: We just discovered that Jmol PNG images inserted in Google Documents preserve their state after saving as zipped HTML. What state are you referring to here? Does Jmol include a script to restore the view as metadata in the PNG? And you mean this metadata is not lost when GDocs saves the document as Jmol? Not that you can just have them be active in the document, but it's still interesting, I think, that at least you can drag them back into Jmol. Does this mean that Jmol can now read PNG files, and show it live, if the PNG contained this state script? Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] try your hand at stereochemistry
On Fri, Oct 14, 2011 at 1:02 AM, Robert Hanson hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/docs/examples-12/isomers.htm What's up with example 4? The MFs don't match... or is that intentional? Just thought of this idea -- will be developing the page to have more examples. Note that under the applets it shows what commands were given. I suggest adding some examples from the CIP papers :) Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] problem when selecting smarts [#6]-[#6]
On Mon, Sep 19, 2011 at 9:46 AM, Martin Guetlein martin.guetl...@googlemail.com wrote: I think the aromatic bonds not should be matched. I think the '~' bond should match any bond and ':' aromatic bonds, but '-' is explicit for single bonds... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) 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 -- BlackBerryreg; DevCon Americas, Oct. 18-20, San Francisco, CA Learn about the latest advances in developing for the BlackBerryreg; mobile platform with sessions, labs more. See new tools and technologies. Register for BlackBerryreg; DevCon today! http://p.sf.net/sfu/rim-devcon-copy1 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol/MediaWiki use in templates?
Hi MediaWiki-plugin users,
while something like jmolSmilesCC/jmolSmiles works fine, when I
try to use this in a Template environment, like with:
jmolSmiles text=3D (Jmol){{{Has Smiles|}}}/jmolSmiles
it does not work... the {{{Has Smiles|}}} is properly set, but the
applet gets not the SMILES but a {{{Has Smiles|}}} string...
How can I get this to work?
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
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Re: [Jmol-users] Jmol/MediaWiki use in templates?
On Wed, Sep 14, 2011 at 10:09 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
jmolSmiles text=3D (Jmol){{{Has Smiles|}}}/jmolSmiles
I think a similar thing is happening with
jmolFile{{{CMLFile|}}}/jmolFile which now gives me this exception:
Catchable fatal error: Argument 1 passed to Article::__construct()
must be an instance of Title, null given, called in
/var/www/toxbank/mediawiki/w/extensions/Jmol/Jmol.body.php on line 690
and defined in /var/www/toxbank/mediawiki/w/includes/Article.php on
line 52
Egon
--
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Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
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PubList: http://www.citeulike.org/user/egonw/tag/papers
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Re: [Jmol-users] Installing jmol as extention to mediawiki
On Wed, Sep 14, 2011 at 7:05 AM, Brian Salter-Duke b_d...@bigpond.net.au wrote: On Wed, Sep 14, 2011 at 12:44:11AM +0200, Angel Herr?ez wrote: https://wiki.ch.ic.ac.uk/wiki/index.php?title=User_talk:Rzepa1 All applets in there work for me: That's in Fiirefox 6.0.2, WinXP, Java 1.6.0_27 Works for me also on Ubuntu with Firefox. Debian Testing with Google Chrome is fine too. Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) 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 -- BlackBerryreg; DevCon Americas, Oct. 18-20, San Francisco, CA Learn about the latest advances in developing for the BlackBerryreg; mobile platform with sessions, labs more. See new tools and technologies. Register for BlackBerryreg; DevCon today! http://p.sf.net/sfu/rim-devcon-copy1 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] OT (a bit): C-I-P R/S assignments in 3D
Hi all, On Sun, Jul 31, 2011 at 2:12 AM, Robert Hanson hans...@stolaf.edu wrote: On Sat, Jul 30, 2011 at 3:42 PM, Richard Ball r...@ellerbach.com wrote: Egon, what do you recommend? R,S stereochemistry is a very complex algorithm. I have a limited implementation in the CDK of the published algorithm, but still we get a good amount of fails. The algorithm is not written by an information specialist, leading to nasty rules that are difficult to implement efficiently. For example, rules that resolve R,S based on the R,S value of other stereocenters, or rules that are based on E,Z stereochemistry. Even more interesting are the rules that state that R,S is decided by the R,S of the atom itself. Like If I am R, then I am R indeed, rather than If I am S, then I should be R, which is not possible, so I am not S :) In short: the rules are nasty. The CDK gets 98.5% right for molecules with one stereocenter, but this goes down for more complex molecules. The lack of a good, Open gold standards is not helping here. That said, other Open Source software that implements (part of) the rules include OpenBabel and OPSIN. With the CDK and the online resolver, we have a few tools to compare against each other. I would advice against trying to implement these rules, particularly because they are mostly needed for coming up with IUPAC names, which Jmol does not do anyway. But then again, I have said that before, only encouraging to you pick up the challenge ;) Grtz, Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) 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 -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] OT (a bit): C-I-P R/S assignments in 3D
On Sun, Jul 31, 2011 at 10:54 PM, Richard Ball r...@ellerbach.com wrote:
Thanks Mike. The problem I want to provide a solution for (assuming there is
one) is: if someone has/gets a .mol file with a complex multi-stereocenter
molecule how can they get the R/S assignment for the particular atoms in the
.mol file while retaining the identity of those atoms.
The CDK can do this starting from SMILES with @ and @@ annotation.
I have used code like this (using Groovy, a Java dialect):
IMolecule mol = sp.parseSmiles(smiles)
IterableIStereoElement stereos = mol.stereoElements()
MapIAtom,ILigancyFourChirality stereoList = new
HashMapIAtom,ILigancyFourChirality();
for (IStereoElement stereo : stereos) {
if (stereo instanceof ILigancyFourChirality) {
ILigancyFourChirality ligancy = (ILigancyFourChirality)stereo;
stereoList.put(ligancy.getChiralAtom(), ligancy);
}
}
print mol + id + :
try {
for (IAtom atom : mol.atoms()) {
if (stereoList.containsKey(atom)) {
rsChirality = CIPTool.getCIPChirality(mol, stereoList.get(atom));
print + rsChirality +
}
}
} catch (StackOverflowError e) {
print StackOverflow;
// e.printStackTrace()
}
Egon
--
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Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
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Re: [Jmol-users] 3D pH change simulation?
Hi Eric, On Sat, Jun 18, 2011 at 11:59 PM, Eric Martz ema...@microbio.umass.edu wrote: Does anyone know of an animation simulation (atomic coordinates) for changes in 3D protein conformation (or amino acid conformation) due to changes in pH? I took the liberty to cross-post your question on BioStar. There is a considerable number of bioinformaticians there, but not much response, though there is a comment from someone who found your question interesting, and started searching in literature: http://biostar.stackexchange.com/questions/9392/animation-of-changes-in-3d-protein-conformation-due-to-ph-change Grtz, Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense.. http://p.sf.net/sfu/splunk-d2d-c1 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol Molecular Orbital Viewer
On Thu, May 19, 2011 at 3:45 PM, Robert Hanson hans...@stolaf.edu wrote: I've done a bit of work on my demo page for viewing molecular orbitals and turned it into the Jmol Molecular Orbital Viewer. See http://stolaf.edu/people/hansonr/jmol/mo Filled is green, empty is red? Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) 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 -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] IRC chat -- Jmol in Wikipedia 30 minutes.
On Tue, Apr 12, 2011 at 4:32 PM, Robert Hanson hans...@stolaf.edu wrote: irc://chat.freenode.net:8001/wikichem to start at 1500 UTC. Feel free to join us. Options for Jmol in Wikipedia. Did you try: http://webchat.freenode.net/ Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) 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 -- Forrester Wave Report - Recovery time is now measured in hours and minutes not days. Key insights are discussed in the 2010 Forrester Wave Report as part of an in-depth evaluation of disaster recovery service providers. Forrester found the best-in-class provider in terms of services and vision. Read this report now! http://p.sf.net/sfu/ibm-webcastpromo ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] super-easy method to insert a Jmol applet into a web page or email message
On Thu, Apr 7, 2011 at 1:51 PM, Robert Hanson hans...@stolaf.edu wrote: Otis Rothenberger and I have been working on ways to improve the accessibility of Jmol to novice users, and I think we have something. Please check this out: http://chemapps.stolaf.edu/jmol/jmol.php Nice! Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) 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 -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] molecular orbital linear combinations
Bob, nice! On Wed, Feb 9, 2011 at 6:43 PM, Shore, Jay jay.sh...@sdstate.edu wrote: I like it a lot – thank you for developing it. Interestingly, on my MacBook (10.6.6) the slider works with Firefox (4.0b1) but not with Safari (5.0.3) nor Chrome (9.0.597.94 beta). Firefox (as IceWeasel) 3.6.13 is fine, but Chrome (9.0.597.84 (72991) Debian 6.0) does not work for me either, wrt the sliders. Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet 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 -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] PubChem SDF
2011/1/18 Angel Herráez angel.herr...@uah.es: Just my 2 cents: Evidently, a fair number of PubChem's sdf's have partial charge data. I see aproblem here. The format shown in your example is not according to SDF spec (I think it does not suppor partial charge, only formal charge). How so? The file looks fine to me. The partial charges are stored in custom data fields... So if Jmol is made to support reading that, it is not really SDF import. That should be made clear. Now, PubChem is that common that it would not be bad to add support for the 'PUBCHEM_MMFF94_PARTIAL_CHARGES' data field... If peope are worried that there will be an explosion of supported common data fields, then it may be an option later to use Jmol script to tell the SD file reader to parse fields as such; something like: set symyxSDreadPropertyAs PUBCHEM_MMFF94_PARTIAL_CHARGES partialCharge (I guess partialCharge will match an existing script keyword reflecting the partial charge, but too lazy right now to look up the exact phrase...) While certainly possible, it is indeed a bit ridiculous to not read these partial charges, and having to use a JS SD files parser for that... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet 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 -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] utilisation de jmol avec ubuntu
On Fri, Jan 14, 2011 at 11:42 AM, philippe philippe.maill...@wanadoo.fr wrote: pouvez vous m'indiquer la procédure pour installer Jmol sous ubuntu pour visualiser des molécules You just download the Jmol.jar and start it from the command line with Java: $ sudo aptitude install openjdk-6-jre wget unzip $ cd /tmp $ wget http://downloads.sourceforge.net/project/jmol/Jmol/Version%2012.0/Version%2012.0.27/Jmol-12.0.27-binary.zip $ unzip Jmol-12.0.27-binary.zip $ cd jmol-12.0.27/ $ java -jar Jmol.jar Hoping that helps (and apologies for not answering in French), Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet 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 -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] utilisation de jmol avec ubuntu
On Fri, Jan 14, 2011 at 1:32 PM, philippe philippe.maill...@wanadoo.fr wrote: Just a last question, I may open an plug-in chime with Jmol. Jmol has a scripting language quite similar to that of Chime, but which has evolved enormously since the Chime days... is that what you mean? Documentation on the scripting language can be found here: http://jmol.sourceforge.net/docs/ There also used to be a tool to convert Chime script into Jmol script, but not sure if that still exists... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet 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 -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol on French TV :)
Hi Nico, On Wed, Nov 24, 2010 at 9:39 PM, Nicolas Vervelle nverve...@gmail.com wrote: A French medical TV show has just used a picture of THC rendered with Jmol for a few seconds. Not much, but that's still nice to know. The broadcast is available for a few days at http://www.france5.fr/allo-docteurs/index-fr.php?page=playerid_article=834 A simple display is visible at 01:42 for a few seconds. Credits are at the end 24:45 with the address of Jmol website. The link works, but the video does not :( I get on hold for 35 seconds, and then only get a white video canvas :( Linux Chrome and Firefox... Has a new wiki page been put online already? ;) Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol on French TV :)
On Sun, Nov 28, 2010 at 11:26 AM, Nicolas Vervelle nverve...@gmail.com wrote: The link works, but the video does not :( I get on hold for 35 seconds, and then only get a white video canvas :( It's working for me : 35 seconds of ads, then video canvas where I click on play (I had to click twice) OK, got it working in Konqueror :) It's a brief appearance, but fun nevertheless... now waiting for the final seconds of the report... (nice program, BTW!) Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] embed Jmol in a google site
2010/11/4 Jan Halborg Jensen jhjen...@kemi.ku.dk: has anyone succeeded in embeding an interactive Jmol model in a google site web site? I just asked the other day about using it on blogger.com (=Google) hosted blogs: http://blueobelisk.shapado.com/questions/what-is-the-simplest-way-of-using-jmol-in-a-blogger-com-blog Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 -- The Next 800 Companies to Lead America's Growth: New Video Whitepaper David G. Thomson, author of the best-selling book Blueprint to a Billion shares his insights and actions to help propel your business during the next growth cycle. Listen Now! http://p.sf.net/sfu/SAP-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [Jmol-developers] Worrying news for Mac users!
On Fri, Oct 22, 2010 at 12:16 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote: http://www.theregister.co.uk/2010/10/21/apple_threatens_to_kill_java_on_the_mac/ As of the release of Java for Mac OS X 10.6 Update 3, the version of Java that is ported by Apple, and that ships with Mac OS X, is deprecated, I think it's not that bad... there is OpenJDK (by Oracle), and seems to be available for OS/X: http://lists.apple.com/archives/Java-dev/2010/Oct/msg00248.html (Dated yesterday...) Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [Jmol-developers] Worrying news for Mac users!
On Fri, Oct 22, 2010 at 12:33 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote: http://lists.apple.com/archives/Java-dev/2010/Oct/msg00248.html That expresses future aspirations, rather than testable reality. There is nothing for OS X at http://openjdk.java.net/ You can find instructions floating around on the web on how to build it... this is one hit: http://confluence.concord.org/display/CCTR/Build+OpenJDK+Java+1.7.0+on+Mac+OS+X+10.5 The argument is that implementing Java for OS X would almost certainly require Apple to release source code for the graphical implementations. If that does not happen, then the actual experience on the Mac may become a poor one. True. Just like we have seen with the Classpath libraries... Well, you only payed minimal money for OS/X, so what can you expect? ;) Jobs appears to want to take OS X towards iOS, which is away from using a mouse and towards using gestures. I think that adapting Java for that sort of environment is going to require major work. Yeah, that is one good reason for Jobs to drop Java... of course, if he would have gone Open Source, he could have shared this burden... Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac Java Update
On Thu, Oct 21, 2010 at 3:17 PM, Philip Bays pb...@saintmarys.edu wrote: Anyone apply the Java update released yesterday? If so, did it break anything? Somewhat related, but also somewhat OT... have people been using OpenJDK on OS/X? Is that possible yet, as it seems Java will phase out their own JVM [0]... Egon 0.http://apple.slashdot.org/story/10/10/21/125222/Apple-Deprecates-Their-JVM -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [Jmol-developers] feature request: complexer hybrid orbitals
On Wed, Sep 1, 2010 at 11:05 PM, Robert Hanson hans...@stolaf.edu wrote: done. I retro-added it to 12.0, just because. Jmol 12.1.9 and 12.0.11 will have sp3d and sp3d2 hybridizations. See documentation for details. Yeah, I saw it in the changelog yesterday! Cool! I will blog about this asap... the biggest problem here is to create a simple example smallest molecule with those hybridizations :) Many, many thanx! Egon -- Dr E.L. Willighagen Post-doc @ Uppsala University (only until 2010-09-30) Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and crystallography: the paper
On Thu, Sep 2, 2010 at 9:21 PM, Robert Hanson hans...@stolaf.edu wrote: This just in! Congrats! Egon -- Dr E.L. Willighagen Post-doc @ Uppsala University (only until 2010-09-30) Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg 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 -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] FW: Problem running Jmol 12.0 application in Linux
On Fri, Aug 20, 2010 at 5:53 AM, Robert Hanson hans...@stolaf.edu wrote: Thank you, Paul, for contacting us about this error. Looks like we had a bug that only appears for first-time users. Ah, so it was a folder that did not exist? Egon -- Dr E.L. Willighagen Post-doc @ Uppsala University (only until 2010-09-30) Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problems launching Jmol 12.0.6 in Linux and Mac OS X
Hi Paul, On Fri, Aug 13, 2010 at 3:01 PM, Paul A Craig pac8...@rit.edu wrote: I am trying to run Jmol on my LInux 9.10 computer and keep getting this error message. I am new to Linux and am not a java programmer. I see the same problem on my Mac. I am running Ubuntu 10.04 with Java 1.6.0_18 and can boot Jmol 12.0.6 fine... java.lang.NullPointerException at java.awt.Component.setLocation(Component.java:1904) at org.openscience.jmol.app.jmolpanel.JmolPanel.init(Unknown Source) at org.openscience.jmol.app.Jmol.init(Unknown Source) at org.openscience.jmol.app.jmolpanel.JmolPanel.getJmol(Unknown Source) at org.openscience.jmol.app.jmolpanel.JmolPanel.startJmol(Unknown Source) at org.openscience.jmol.app.Jmol.main(Unknown Source) Exception in thread main java.lang.NullPointerException at org.openscience.jmol.app.jmolpanel.JmolPanel.startJmol(Unknown Source) at org.openscience.jmol.app.Jmol.main(Unknown Source) The stacktrace seems to originate from line 270 in JmolPanel.java, but I am not sure why the JFrame jmolFrame = new JFrame(); at line 262 would not have worked... You seem to be running with a Sun/Oracle JVM too, so that should be fine too... In the same folder, can you please try: java -jar Jmol.jar ? Egon -- Dr E.L. Willighagen Post-doc @ Uppsala University (only until 2010-09-30) Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Fwd: Java embedding plugin
On Wed, Aug 11, 2010 at 6:08 PM, Philip Bays pb...@saintmarys.edu wrote: I just got this response from the author of the Java Embedding Plugin that the Mozilla browsers use to implement Java applets on the Mac. A solution may be in sight:=) Great! Thanx for getting in contact with them! Egon -- Dr E.L. Willighagen Post-doc @ Uppsala University (only until 2010-09-30) Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Sharing of Jmol scripts?
Hi all, I saw some interesting emails lately on the scripts and sorts... has anyone yet considered using MyExperiment.org for sharing useful Jmol scripts? Would that be an interesting platform to share Jmol scripts like: Show the heme groups in protein X. Demonstrate the hydrogen bonding framework in alpha helices. Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] handy guide to new Jmol 12.0 features
On Wed, Jul 28, 2010 at 4:10 PM, Robert Hanson hans...@stolaf.edu wrote: Here's a listing of all the new capabilities of Jmol 12.0, categorized: http://chemapps.stolaf.edu/jmol/docs/examples-12/new12.htm Congrats, Bob! Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Fwd: [Bug 581717] Firefox does not read java cache correctly
On Tue, Jul 27, 2010 at 1:58 PM, Robert Hanson hans...@stolaf.edu wrote: we just need to have someone with a Mac use their Java Preferences App to set the preference for applets to Java 1.5 and see if it fixes the problem. I think it will. If so, then clearly it IS a Java 1.6 issue. I would normally have asked Arvid, Jonathan or Ola here, but they are all on holiday right now... :( Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://ad.doubleclick.net/clk;226879339;13503038;l? http://clk.atdmt.com/CRS/go/247765532/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] idtf output for polyhedral structures
On Thu, Jul 15, 2010 at 2:59 PM, Van der Lee avder...@univ-montp2.fr wrote: Bob's fix worked well (thanks!): http://www.dicoscouts.x10hosting.com/perez.pdf Can anyone suggest a reader for Linux that supports this live content? I tried Okular [0], but that showed an empty slide :( Egon 0.http://okular.kde.org/ -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- 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] HTML5 and WebGL
On Thu, Jul 15, 2010 at 5:04 AM, Robert Hanson hans...@stolaf.edu wrote: Can someone explain to me how the combination of HTML5 and WebGL is a replacement for Java? It is not so much the Java language as it is the Applet design... the applet concept requires a plugin to be installed (with the Java VM), while a JavaScript VM comes by default with any browser... (yes, if only they had made BeanShell the scripting language... or Groovy, or ...) Is the idea there that HTML5 somehow (via on-the-fly compiling? via pre-compiled equivalents of Java?) can reach the sort of speeds that people need for molecular graphics? Or is this just a dream? I'm just not finding anything out there that suggests it's any more than JavaScript with a 3D canvas. It's true that it would be nice to have built-in 3D graphics, and I can see how in some limited fashion this could be useful, but there's a lot besides rendering that is done in the process of molecular visualization. Construct an MO? Apply symmetry? I fully agree that the JavaScript versions have not catched up with Jmol, and with your speed, they will find it hard to keep up too :) But, the point is that the applet environment is getting dated... not much new developments there... no race between Google, Nokia, Apple, Mozilla Foundation to produce the fastest VM... JChemPaint faces the same 'problem'... will it get overtaken by JavaScript solutions... Mind you, I like my iPhone. It's a great phone. I hate the one I do not have: it does not do Java... Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- 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
[Jmol-users] fwd: Should I use Jmol or ChemDoodle for developing a 3d application?
See: http://blueobelisk.shapado.com/questions/should-i-use-jmol-or-chemdoodle-for-developing-a-3d-application Eg. -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- 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] [BlueObelisk-SMILES] News flash: Jmol reads SMILES into 3D format.
On Fri, May 28, 2010 at 7:52 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote: On May 28, 2010, at 10:22 AM, Robert Hanson wrote: This uses a web service at Indiana University http://cheminfo.wikispaces.com/smi23d that appears to use PCMODEL for its converter. The idea is similar to the way = goes to the RCSB site. The web service is based on smi23d (http://www.chembiogrid.org/cheminfo/smi23d ) which itself is derived from PCMODEL Is there a tutorial describing: 1. how people can host this smi23d service themselves? 2. how to configure Jmol to use that 'mirror' ? Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol model kit and docking
On Fri, May 28, 2010 at 4:30 AM, Robert Hanson hans...@stolaf.edu wrote: 137. set picking dragMinimizeMolecule -- responsive docking With Jmol 12.0.RC15 you can move a small molecule around and watch it react to its environment. Grab the caffeine molecule and move it toward the protein. Holding SHIFT down allows rotation. CTRL-Z undoes an action; CTRL-Y does a redo. Can you perhaps add an option to automatically calculate H-bonding and perhaps ionic interactions after the minimization is done, to visualize how it is bound in the active site? Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [BlueObelisk-SMILES] JmolSmilesApplet.jar
Hi Bob, On Thu, May 13, 2010 at 5:12 AM, Robert Hanson hans...@stolaf.edu wrote: Probably what we should do is write a simple open-source version of JME to provide a frame to JmolSmilesApplet. It's too bad that Peter's work is not extensible in that regard. Peter, you sure you don't want to do this? But it would be a nice project - either to use a streamlined version of JChemPaint or just start from scratch. I mostly like Peter's interface, but there are some very good ideas in JChemPaint as well. Suggestions? What we are looking for is a very small, simple interface. Nothing fancy. If it comes from CDK it will need to be VERY highly streamlined. I'll try to find some time for the further refactoring of the CDK-JChemPaint architecture, and work on a minimal applet. Interestingly, my first version was 120K, then I refactored Jmol and got it down to 43K, then I did a clean build and discovered it was only 39K. Interesting process. Impressive! This only strengthens my opinion with the right effort we can get a small JChemPaint applet too. Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol smarts/smiles upgrade
Hi Bob, I'm impresses, once more... and don't want to spoil the news of this powerful API! But... On Wed, May 5, 2010 at 8:07 PM, Robert Hanson hans...@stolaf.edu wrote: select smarts(C(F)[...@](Cl)H) ... this molecule is not chiral... How does your lib handle the SMILES listed by Noel: http://baoilleach.blogspot.com/2009/03/clockwisdom-of-smiles-part-ii.html Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol smarts/smiles upgrade
On Wed, May 5, 2010 at 8:17 PM, Egon Willighagen egon.willigha...@gmail.com wrote: On Wed, May 5, 2010 at 8:07 PM, Robert Hanson hans...@stolaf.edu wrote: select smarts(C(F)[...@](Cl)H) ... this molecule is not chiral... But then again, it's a SMARTS, not SMILES... so, it's fine that the chiral atom lacks the fourth non-hydrogen side chain... /me is embarrassed... Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol smarts/smiles upgrade
On Wed, May 5, 2010 at 9:03 PM, Robert Hanson hans...@stolaf.edu wrote: those should all be fine. They are similar to all the ones I tested. It's a full range of [...@1] [...@th2] [C@@] [...@h] etc. The parser accepts the defaults for two-, four-, five-, and six-bond situations (AL, TH, TP, OC), but the matcher does not yet process SP, TP, or OC. I'm figuring I will implement just the minimal versions of those. Shouldn't be too terribly difficult. Bob++ Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol smarts/smiles upgrade
On Thu, May 6, 2010 at 4:34 AM, Robert Hanson hans...@stolaf.edu wrote: What the heck! Might as well do them all! So, can these chiral SMILES also be used to create a 3D model? Where the stereo is correctly applied? Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Fwd: Java 1.5
On Wed, Apr 28, 2010 at 3:59 PM, Robert Hanson hans...@stolaf.edu wrote: I propose that Jmol 12.0 officially require Java 1.5. This will allow easy expansion of several features, including parallel processing, which we just introduced for isosurface creation. Java5 is out of service too, and at least Ubuntu and Debian no longer ship Java5. I think this is also the case for Fedora/RedHat. So, requirement of at least 1.5 sounds good to me for Linux platforms. Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Fwd: Creating PNGs from Jmol
Nice blog post with a small request (please leave as comment in blog too): http://sea36.blogspot.com/2010/04/creating-pngs-from-jmol.html I think Sam's question is about the following: is it possible with the Jmol.js to show a (pre-compiled?) PNG image of a structure which can be clicked to open (replace with Ajax?) the image with the applet? Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Chime to Jmol
On Wed, Apr 21, 2010 at 8:42 PM, Robert Hanson hans...@stolaf.edu wrote: I know I'm not the first to think of doing this -- what else is out there in this regard? There used to be a script to convert a Chime script into a Jmol script... have you used that? Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Another publication about Jmol...
On Fri, Apr 9, 2010 at 11:29 PM, Jonathan Gutow gu...@uwosh.edu wrote: J. Chem. Ed. has just published a brief description of Jmol and the export to web function as well as archived a copy of the tutorial I put together. I'll add the link to the Wiki, but post it here in case anybody cares. J. H. Gutow, Easy Jmol Web Pages using the Jmol Export to Web Function Journal of Chemical Education WebWare. Publication Date (Web): April 8, 2010. link: http://pubs.acs.org/doi/abs/10.1021/ed100283v Nice! Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol -- two major advances
Bob, On Wed, Apr 7, 2010 at 5:37 PM, Robert Hanson hans...@stolaf.edu wrote: I'm sure there is. And if VMD is any example, the use of GPUs would vastly increase performance. It would be a great project for someone to explore. Since I know nothing about parallel processing, I'm not the one to take it on. How is a Jmol view (Image) currently calculated? Wasn't this done pixel by pixel (that's what I remember, but I might be mixing up things)? Would it then not be possible to divide the Image into 2 parts and calculate each in 2 threads (etc)? Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [PhyloSoC] Google Summer of Code proposal for 3D protein-structure evolution visualization
Hi Hilmar, Bob is the current code wizard... my Jmol code is long past history, but we are using it in Jmol, and that needs an overhaul anyway... I have been GSoC mentor in the past already, but could be available for co-mentoring... Bob, do you fancy a Google SoC T-shirt? Egon On Fri, Mar 26, 2010 at 8:51 PM, Hilmar Lapp hl...@nescent.org wrote: Hi Egon, we're trying to recruit a co-mentor for Chris. Could you fancy yourself co-mentoring? It'd be great to have you on board with this project and with the NESCent community in the larger sense. -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Good news/bad news/good news - orbitals
On Thu, Mar 25, 2010 at 2:58 PM, Robert Hanson hans...@stolaf.edu wrote: This is fixed, and we will get a release out this weekend I hope. Bob++ Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Google Summer of Code proposal for 3D protein-structure evolution visualization
Hi Christian, On Fri, Mar 26, 2010 at 1:32 AM, Christian M Zmasek czma...@burnham.org wrote: I am the main developer of the Archaeopteryx phylogenetic tree viewer (http://www.phylosoft.org/archaeopteryx/). For this year's Google Summer of Code (http://code.google.com/soc/) we developed a proposal to essentially extend Archaeopteryx with Jmol so that it can be used for 3D protein-structure evolution visualization, see: That's great to hear! https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2010#Visualization_of_Protein_3D_Structure_Evolution Members of the Blue Obelisk community have tried in the past to get in as mentoring organization, but that always failed... I was wondering if a Jmol developer or experienced user would be willing to help with this project, as co-mentor. In this case, co-mentoring would mean helping out with questions specific to Jmol (time commitment is expected to be minimal, maybe 1h/week or less for the duration of the program -- 3 months). That means you will have a first full time mentor from the NESCent? Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] black-and-white ORTEP diagrams? (was: CCL: Visualizing Software)
On Mon, Mar 8, 2010 at 2:57 PM, Robert Hanson hans...@stolaf.edu wrote: That's ridiculous. Sorry, but to try to go retro on this is just too strange. :) I agree; don't shoot the messenger. Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] black-and-white ORTEP diagrams? (was: CCL: Visualizing Software)
Hi all, I saw this interesting question on the CCL mailing list: On Tue, Mar 2, 2010 at 9:55 PM, Anthony F wrote: My next question is on visualizing my XYZ files. I have used Avogadro, VMD, and Gabedit. But I want to make diagrams like these: http://bhgroup.lsa.umich.edu/files/u1/ge-prop-ortep.gif I prefer how the ellipsoids have the 3D effect and that everything is in black and white. I don't like how bonds have two different colors in Avogadro and VMD. There is a nice tutorial by the IUCR that shows how ORTEP diagrams can be used: http://journals.iucr.org/services/help/jtkt/7.html And I know the scripting language can be used to change the colors of atoms and bonds... But that would not cover a border around atoms and bonds, I guess, so that we can make them all white-on-white... Has someone tried to make black-and-white ORTEP diagrams with Jmol? Kind regards, Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol-in-the-movies wiki section?
Hi all, our wiki has sections for Jmol-in-publications (getting overcrowded :), Jmol-in-wiki's, etc... Just got this (old) link with Jmol (via Bioclipse) in the movies :) http://divby0.blogspot.com/2008/10/eclipse-photoshop-challenge-better-than.html Happy new year all! Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JMol server side
Nina, On Sun, Dec 27, 2009 at 11:55 AM, Nina Jeliazkova n...@acad.bg wrote: I am looking for a guide or examples to use JMol in headless mode, for generating images on the server side. check out the answer on the Blue Obelisk Exchange: http://blueobelisk.stackexchange.com/questions/38/how-do-i-automate-the-generation-of-3d-images-of-molecules/40#40 Have a look at the source code of the Jmol.java to see how to run the script and not fire up the GUI (see the -n option). pedanticIt's Jmol, with a lower case 'm' :)/pedantic Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and multiTouch
On Fri, Dec 25, 2009 at 5:01 PM, Robert Hanson hans...@stolaf.edu wrote: Did I forget to send this? This video demonstrates a first go at incorporating multi-touch capability into Jmol. http://www.youtube.com/watch?v=7x8uDRQKIg0 I had not seen it yet. Nice video! Cool hardware... Some time ago there was someone who used a Wii remote control and a infrared light, and two reflectors on his fingertips... and hooked up the Wiimote input to this kind of multitouch input... might be a nice mash up :) How does it work on the API level? How do you get the SparshUI input linked to the running Jmol? Using script? Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] what is Jmol for?
On Wed, Dec 16, 2009 at 9:22 PM, Robert Hanson hans...@stolaf.edu wrote: But I agree, the business with axes and tics and such is pretty far afield of the core Jmol mission. Not sure if ticks are must used in crystallography, but axes most certainly... I also use the axes visualization in some graphics for a book chapter that is about finished on 3D molecular representation... (which I will email about when published). Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] New chemical software
On Fri, Nov 20, 2009 at 5:08 PM, Robert Hanson hans...@stolaf.edu wrote: Jmol is GPLP That would be LGPL :) Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] feedback appreciated
On Wed, Nov 18, 2009 at 10:38 PM, Jeff Hansen jhan...@depauw.edu wrote: Lets just go extreme with this. Make every side of the applet available for adjusting something. I could see zoom, Z-rotation, slab, atom size. Why not just make it configurable so a little javascript or Jmol script can assign a property to a particular side and we can adjust whatever we want to adjust? Kind of a built in slider. And I assume the area would 'highlight' a bit when I am in the right spot, as visual feedback? A bit less black than black, a bit less white than white, or so? Or always a bit more yellowish? Just to get a good feeling for that 2%? Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] feedback appreciated
On Thu, Nov 19, 2009 at 12:14 AM, Robert Hanson hans...@stolaf.edu wrote: Why not just make it anywhere you want? any function? Say, on top/around of a certain atom, bond or secondairy structure? Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] feedback appreciated
On Thu, Nov 19, 2009 at 12:27 AM, Robert Hanson hans...@stolaf.edu wrote: Hmm, I was thinking more along the lines of within a certain area of the window. You can always trap a pickCallback for atoms. True. I did not think of it that this could be done on a purely Jmol script level too... how does that work? Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] feedback appreciated
Nice!
On Thu, Nov 19, 2009 at 12:43 AM, Robert Hanson hans...@stolaf.edu wrote:
function testit {
print _atomPicked
}
set pickCallback jmolscript:testit;
Egon
--
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now. http://p.sf.net/sfu/bobj-july
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[Jmol-users] Coolest 2009 Nature Chemistry paper :)
Thanx, Henry! http://www.nature.com/nchem/journal/v1/n7/media/nchem.373_jmol.html Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Can I get the Jmol content as CML?
Hi all, is Jmol still able to save the content? For example as CML or perhaps MDL molfile or XYZ? Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Can I get the Jmol content as CML?
On Fri, Oct 30, 2009 at 3:03 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote: As it happens, Bob and I have been having a discussion about eg saving XYZ (with vibrational vectors). Bob's documentation does describe the process, although of course one has to use the signed applet to use the write command if doing so from a Web page. Ah, right... 'write COORDS MOL file' is what I need. However Egon, are you asking whether eg the Jmol DOM content model which stores the coordinates has an internal output stylesheet that can perform the conversion to eg CML, ie eg Molfile in, CML out, in the manner of openBabel? Yes, 'write COORDS CML file.cml' would be nice... but MDL molfile is a good enough start. Bob has also described his XMLised version of jvxl. Yeah, we were talking about that... I presume an XML version of the Rasmol script is a far greater undertaking? Indeed. But not what I am looking for right now. Thanx for your ideas! (And I feel stupid for looking at the Jmol source code, instead of the far more informative interactive help! :) Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Calculating volume within Van der Waals surface.
On Wed, Sep 2, 2009 at 8:11 PM, N David Brownhubd...@googlemail.com wrote: Given the 677 compounds tested and the proximity to the TSAR values, I think that's an odd comment. It's an approximation, true, but for the drop in computational cost I find the accuracy astounding. So, just out of curiosity... What size of error are we talking about here? What are we comparing against anyway? What is the empirical vanderwaals volume of some molecule? Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Fwd: info
On Sun, Aug 2, 2009 at 9:06 AM, Robert Hansonhans...@stolaf.edu wrote: Can someone help here? I think he registered after my reply. Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Fwd: Jmol 11.8.RC4 and the GRC
Hi Bob! On Sat, Aug 1, 2009 at 7:46 AM, Robert Hansonhans...@stolaf.edu wrote: The 2009 Gordon Research Conference on Visualization in Science and Education is over. It was unbelievably cool. It's strict policy not to discuss anything that was at that meeting, so please don't ask me to do that. :) I'm sure some ideas will just make Jmol in the next months, without us ever knowing Gordon was involved... everytime you say I just had a vision of unknown source of this cool feature... :) However, some ideas were transmitted to me during the meeting from Jmol users, and I did have a few hours to work on Jmol here and there outside of the actual conference hours, so there are a few new features in Jmol 11.8.RC4 even though I try not to do that with a release candidate. Three new features and one crazy idea of note: Mouse-movable labels Lone pairs and radicals This I particularly like... I guess this is not yet reflected in the model, is it? That is... if CML contains LP or radical information, is this directly visualized yet? Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Third Release Candidate for Jmol 11.8
Hi all, I just uploaded Release Candidate 3 for Jmol 11.8 with the following changes: # code: more efficient VRML export # new feature: set helixStep 1,2,3,... sets step for quaternion-based analysis of structure -- see 1C4D # bug fix: 1C4D has [FOR] -- not accepted # bug fix: color isosurface red translucent prior to isosurface command causes null pointer exception # new feature: isosurface select() SET n where n is an integer 1,2,3... that selects which set is to be displayed and counted for area or volume # bug fix: spacegroup reading when center of molecule is not in unit cell can cause bonding errors # new feature: isosurface area for subsets -- use isosurface area select(oxygen) sasurface colorscheme sets # bug fix: draw OFF in state script is not selective Have a nice weekend! Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Does Jmol Support Output for Use with 3D Glasses?
On Fri, Jul 3, 2009 at 10:14 AM, Egon Willighagenegon.willigha...@gmail.com wrote: Rich asks in his blog: http://depth-first.com/articles/2009/07/02/dear-lazyweb-does-jmol-support-output-for-use-with-3d-glasses Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol Version 11.6.25
Hi all, bug fix release 11.6.25 for the stable Jmol series has just been made available on SourceForge with the following changes: # bug fix: select model=1 does not work (since 11.6.RC17!) # bug fix: dipole offsetside not working for molecular dipole (EVER!) # bug fix: 2 pixels off in y for labels. Don't know why I thought that was necessary in Text.java::setBoxXY. # bug fix: dipoles cannot be colored by name # bug fix: dipole settings not accessible via wildcards # bug fix: gzipped gzip file not read properly. (Jmol-FAH files) # bug fix: Crystallographic Information File not recognized. Greetings, Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol Prerelease 11.7.46
Hi all,
a new Jmol prerelease has been uploaded to SourceForge, bringing these
changes as listed in the changelog:
# bug fix: select model=1 does not work (since 11.6.RC17!)
# new application: JmolData.jar
# This application completely disallows any display -- it is totally formless
# There are no Java Swing JFrames involved, no dialogs, no popup menus,
# no display, no shapes, no labels, no echos -- just the model data.
#
# bug fix: command-line jmol scripts not exiting jmol upon an error condition
# argh. FOR broken in 11.7.45
# new feature: helix(resno or {atomExpression},type)
# given x = C-alpha, C-carbonyl, or N (depending upon set
quaternionFrame)
# where type =
# point -- nearest point to x on local helix axis
# axis -- quaternion derivative vector normal indicating local helix axis
# angle -- rotation around local heix axis for resno i -- i+1
# radius -- vector normal from local helix point to x
# draw -- draw command for the local helix vector
# note that the axis length is the rise, radius length is the radius,
# and 360 / angle is the pitch of the helix
#
# bugfix: gamess readers crashing if keywords missing from basis options or
control options
# code: findNearestAtomPicked added to JmolViewer
# new feature: VRML exporter displays ribbons and cartoons by
automatically setting hermiteLevel 1 if necessary.
# new feature: VRML exporter recognizes color and normals for isosurface
Kind regards,
Egon
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[Jmol-users] Jmol 11.7.45 released
Hi all,
not too long after the .44 release the changes are piling up again;
see below. Downloads from:
http://sourceforge.net/project/showfiles.php?group_id=23629package_id=142353release_id=693156
# bug fix: load trajectory XXX.cif not applying fractional coordinates.
# bug fix: load trajectory {0 -1 1} not loading any models if first
model has 0 atoms
# (as in certain cif files)
# bug fix: dipole offsetside not working for molecular dipole (EVER!)
#
# code: refactored scriptEvaluator and Jmol.java. Now it is much
simpler
# to create a truly headless Jmol application, where Jmol is being
# used for the investigation of the structure instead of
visualization.
#
# new application: JmolFrameless.jar
# This application completely disallows any display -- it is totally
formless
# There are no Java Swing JFrames involved, no dialogs, no popup
menus,
# no display of any kind.
#
# script editor behaving properly except for a nasty SWING bug that
will
# require recasting this in AWT instead of SWING.
# See http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4353673
#
# new feature: gamessUS reader now reads dipoles and partial charges.
#
# TODO script editor -- search? argh... I knew this would be a can of
worms...
# script editor -- undo/redo works (CTRL-Z, then SHIFT-CTRL-Z or
CTRL-Y)
#
# new feature: drag/drop and file menu-open scripts directly into
editor, from where they can be checked or tested.
# code: refactored readers, allowing for more obvious
initialization/finalization methods
# new feature: App and applet consoles now have editor buttons
# that load scripts into a script editor and allow stepping through
# scripts (and changing values during the pauses) - preliminary only
#
# opens a rough draft ScriptEditor
# new feature: Gamess file reader now translates internal basis set
and calculation
# methods representations into roughly literature standard for
Pople Dunning basis
# sets as well as perturbation, CI and CC calculation methods.
This is dumped to
# calculationType.
# new feature: application console buttons: PAUSE, ?, STEP
# new feature: SHOW TRACE -- reports stack trace
# bug fix: functions with names starting with _ were local instead of
global
# bug fix: 2 pixels off in y for labels. Don't know why I thought that
was necessary in Text.java::setBoxXY.
# new feature: SHOW VARIABLES now gives variable trace through
function stack
# new feature: [Oh, VERY COOL!] You can now pause the app anywhere in
a
# script, do anything you want -- even within functions -- change
variables,
# set parameters, anything -- and then resume with RESUME. Some of us
# have dreamt of having this with JavaScript. Very very useful!
# so, for example:
#
# function testing(i,j) {
# n = 3
# show variables
# pause change any variable and then enter RESUME
# show variables
# }
# testing(3,5)
#
# bug fix: problems with PAUSE/RESUME within App
# bug fix: set ? nonfunctional
# bug fix: unmatched { in quotes in @{ } not properly treated: echo
@{ testing}}
# new feature: strings may start with ' or , like JavaScript:
# x = 'testing'
# print 'there are ' + all.length + ' atoms'
# cd, echo, gotocmd, help, hover, javascript, label, message, and pause
# all are implicitly strings. You CAN use ... but you don't have to,
# and you cannot use '...'. This way the introduction of single quotes
# as an equivalent of double quotes cannot break existing scripts.
-- BH 06/2009
# new feature: print getProperty(PDBInfo,REMARK300)
Egon
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Re: [Jmol-users] Bob traveling to England and Germany
On Mon, Jun 29, 2009 at 5:06 AM, Robert Hansonhans...@stolaf.edu wrote: In case there is anyone in the London/Oxford/Lancaster areas or Berlin/Frankfurt areas who would like to get together and talk about Jmol (or let me give a presentation!), here is my itinerary for July/Aug: July 22 - arrive London July 24 - Lancaster July 25 - Aug 1 Oxford (Gordon Conference on Visualization) Aug 1-4 - Berlin Aug 5-10 - Frankfurt I don't think this overlaps with my schedule, unless you make a stop in the Netherlands, between Oxford and Berlin, or stay three weeks longer in Frankfurt :) BTW, nice prestigious conference! Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol release 11.7.44
On Wed, Jun 24, 2009 at 11:41 AM, Jan H. Jensenjhjen...@kemi.ku.dk wrote: The GAMESS reader sounds very interesting, but I haven't been able to find any documentation on the web? Usually, Bob puts up demos of new features at: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm But I do not see the new GAMESS functionality demoed there... Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol release 11.7.44
Hi all,
with Nico on holiday, I got to honour to make a Jmol release again,
after a very long time of not doing releases :)
I'm pleased to announce the Jmol Prerelease 11.7.44 with the following
changes by the every amazingly productive Bob:
# bug fix: write FRAMES also for trajectories
# new feature: MO LIST or SHOW MO LIST display listing of orbitals for all files
# new feature: GAMESS reader now sets calculationType, orbital type,
and auxiliaryInfo.calculationOptions
# bug fix: select(x;{xxx};...) or for(x;{xxx};...) when {xxx} is empty
returns incorrect result
# bug fix: dipoles cannot be colored by name
# bug fix: dipole settings not accessible via wildcards
# new feature: merging of label() and format() functions -- same in
all respects.
# bug fix: spartan'08 reader not reading vibrations
This being the first time in ages of making Jmol builds, make sure to
cc me personally if I messed up :)
Egon
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Re: [Jmol-users] cool new Jmol features
On Wed, Jun 3, 2009 at 10:20 PM, Robert Hanson hans...@stolaf.edu wrote: see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm Check it out! Nice ! Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] cool new Jmol features
On Thu, Jun 4, 2009 at 9:52 AM, Egon Willighagen egon.willigha...@gmail.com wrote: On Wed, Jun 3, 2009 at 10:20 PM, Robert Hanson hans...@stolaf.edu wrote: see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm Check it out! Nice ! BTW, I get an unexpected exception in step 2 of 17. user-definable atom selector functions. Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JMOL and Wikipedia
On Tue, Jun 2, 2009 at 1:15 AM, Brian Salter-Duke b_d...@bigpond.net.au wrote: On quality, I think that is a different and general concern. We try to not use poor quality images, so we would try to use only good quality Jmol data files. I am happy that we restrict the type of jmol files to a small number, perhaps initially only *.pdb files. Of course we would have to add file extensions for jmol files to the upload process anyway, so we would not need to add all possible file extensions. PDB is not a good format for small molecules; CML would be much better, e.g. by allowing embedding of important information regarding identification of the structure, or adding info on who added that image. Please be specific when you suggest file formats: there are two main areas of interest here: protein (PDB is the de facto standard), small molecules. In both cases, there are many alternative, and PDB as format has, at least, lesser quality than other offerings. I also really don't get the security concerns brought up... sorry, for dropping in on this, but have been involved in talk several years ago too, and if you want Jmol without JavaScript, that is no problem. JavaScript as security problem regarding a Jmol extension for WP is a non-issue. People have been using plain HTML for embedding Jmol in various website for more than 10 years, and I have no clue why this would not be a problem for WP. Please explain. Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
