Bob, this would then mean Jmol really does provide a replacement for MDL CHIME..... Would Jmol then read mol files where all the z coords were zero and be able to generate a reasonable representation?
Robert Prof. Robert J. Lancashire mailto:robert.lancash...@uwimona.edu.jm Department of Chemistry Tel (876) 512 3026 University of the West Indies, Kingston 7 Fax (876) 977 1835 Mona Campus, JAMAICA. http://wwwchem.uwimona.edu.jm/chrl.html ________________________________________ From: jmol-developers-requ...@lists.sourceforge.net [jmol-developers-requ...@lists.sourceforge.net] Sent: Wednesday, April 28, 2010 05:09 PM To: jmol-developers@lists.sourceforge.net Subject: Jmol-developers Digest, Vol 47, Issue 6 Send Jmol-developers mailing list submissions to jmol-developers@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/jmol-developers or, via email, send a message with subject or body 'help' to jmol-developers-requ...@lists.sourceforge.net You can reach the person managing the list at jmol-developers-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Jmol-developers digest..." Today's Topics: 1. 2D/3D project (Robert Hanson) 2. Re: 2D/3D project (Egon Willighagen) 3. Re: 2D/3D project (Jonathan Gutow) 4. Re: 2D/3D project (Angel Herr?ez) 5. Re: 2D/3D project (Egon Willighagen) 6. Re: Java 1.5 (Miguel Howard) 7. Re: 2D/3D project (Robert Hanson) ---------------------------------------------------------------------- Message: 1 Date: Wed, 28 Apr 2010 12:28:23 -0500 From: Robert Hanson <hans...@stolaf.edu> Subject: [Jmol-developers] 2D/3D project To: Jmol Developers <jmol-developers@lists.sourceforge.net> Message-ID: <g2yba9c0bd61004281028x7e2b882bpb1d207bbbf749...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Jmol Developers. I have an idea for a little(?) project and am trying to figure out the best way to do it - and am interested in collaborators, particularly. As you probably know, we have had tremendous success lately with 2D -> 3D conversion using the JME applet. See, for example, the 2D-to-3D link just below the applet at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htmor just http://chemapps.stolaf.edu/jmol/docs/examples-11/JmeToJmol.htm This idea stems from that success. The idea: 1. Add a 2D drawing tool to the Jmol applet that would provide a similar (though expanded) functionality of JME (and, unlike JME, would be open source, of course!). 2. Add functionality to Jmol that would allow storage of the 2D image as a PNG or JPG image with capability to open or drag-drop the image into Jmol and recreate the 2D editor or 3D model directly. 3. Add functionality to Jmol that would allow writing a PNG or JPG image with capability to open or drag-drop the image into Jmol and recreate the 2D editor or 3D model directly. I think the benefits of this are obvious -- you'd be able to put up an image on a web site, open it in 2D, edit it, check the model, edit it again, check the model, save the image, save the model, etc. With regard to JME itself, unfortunately, Peter Ertl is not in a position to release that code. So options involving JME itself are not viable. The JME code is not and probably cannot ever be made open source due to its complicated history. But the good news is that it is a very small, specific task, I think, to do this sort of editing. It really should not be that hard to do. What do you think? Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 2 Date: Wed, 28 Apr 2010 19:45:34 +0200 From: Egon Willighagen <egon.willigha...@gmail.com> Subject: Re: [Jmol-developers] 2D/3D project To: jmol-developers@lists.sourceforge.net Message-ID: <q2s6aeb064b1004281045je1b02b94lcc4f6e0bbb6df...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 On Wed, Apr 28, 2010 at 7:28 PM, Robert Hanson <hans...@stolaf.edu> wrote: > 1. Add a 2D drawing tool to the Jmol applet that would provide a similar > (though expanded) functionality of JME (and, unlike JME, would be open > source, of course!). Like JChemPaint? 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 ------------------------------ Message: 3 Date: Wed, 28 Apr 2010 13:15:05 -0500 From: Jonathan Gutow <gu...@uwosh.edu> Subject: Re: [Jmol-developers] 2D/3D project To: jmol-developers@lists.sourceforge.net Message-ID: <a1cfbbc8-be62-4f2d-bbf3-2b6d8b09e...@uwosh.edu> Content-Type: text/plain; delsp=yes; format=flowed; charset=US-ASCII My question exactly. On Apr 28, 2010, at 12:45 PM, Egon Willighagen wrote: > Like JChemPaint? > > Egon If this were done, might it be best to keep them as separate applications and make sure they can communicate or is it worth folding them into one application? I worry about Jmol getting to be too many things and then not doing anything very well. Right now it is very good at 3D molecule rendering, especially on the web. I think is would be better to reinvigorate Jchempaint as a separate project that plays nice with Jmol. I think Bob Belford had some interest in working on it at one point. Do you remember anything about that Bob H.? Jonathan Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.edu UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow ------------------------------ Message: 4 Date: Wed, 28 Apr 2010 20:22:07 +0200 From: Angel Herr?ez <angel.herr...@uah.es> Subject: Re: [Jmol-developers] 2D/3D project To: <jmol-developers@lists.sourceforge.net> Message-ID: <4bd87ccf.23161.1a6bc...@angel.herraez.uah.es> Content-Type: text/plain; charset="US-ASCII" I've been playing for somewhat long time with connecting JChemPaint for 2D drawing toJmol for 3D rendering. It's over a year that I have a working prototype, but haven't released it public because I was expecting to polish it up. In fact, that's the topic of one of my presentations at BCCE next August in Denton. A few bugs or lack of features in the Javascript API of JChemPaint have refrained my progress with this. Then, JCP v3 was started with quite a reworked engine, and I posed great expectation on it, but haven't been able to solve my pending issues with this new version, so I'm still relying on the old v2. Particularly, addition of explicit hydrogens has been a constant problem. And Jmol minimization heavily depended on the Hs being present in order to be successful. So what I have is a semimanual procedure which is not too user-friendly. I haven't yet had the chance to explore the recent addition in Jmol of calculate hydrogens, which may solve my bottleneck with JCP. I have therefore followed -but couldn't keep pace with- the recent and so very fast developments in connecting JME with Jmol, with excitement but also with a bit of dismay at having lost my chance to be "the first" ;-) Great work, Otis and Bob! My bet for JCP was based, of course, on it being open source. I guess the connection could be done at the Java level but my knowldege limited me to using Javascript. ------------------------------ Message: 5 Date: Wed, 28 Apr 2010 20:30:19 +0200 From: Egon Willighagen <egon.willigha...@gmail.com> Subject: Re: [Jmol-developers] 2D/3D project To: jmol-developers@lists.sourceforge.net, cdk-jchempa...@lists.sourceforge.net Message-ID: <o2p6aeb064b1004281130uce0a1391h16375a8855cc8...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 cc: cdk-jchempa...@lists.sf.net Bob, Angel, 2010/4/28 Angel Herr?ez <angel.herr...@uah.es>: > A few bugs or lack of features in the Javascript API of JChemPaint ?have > refrained my > progress with this. Then, JCP v3 was started with quite a reworked engine, > and I posed great > expectation on it, but haven't been able to solve my pending issues with this > new version, so > I'm still relying on the old v2. Particularly, addition of explicit hydrogens > has been a constant > problem. And Jmol minimization heavily depended on the Hs being present in > order to be > successful. ?So what I have is a semimanual procedure which is not too > user-friendly. > I haven't yet had the chance to explore the recent addition in Jmol of > calculate hydrogens, > which may solve my bottleneck with JCP. can you please reiterate the problems with the JCP v3 methods visible to JavaScript? Bob, with the JME/Jmol setup, which does the initial 3D geometry? JChemPaint could do that, but makes the applet larger... (particularly, if the ring database is used 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 ------------------------------ Message: 6 Date: Wed, 28 Apr 2010 16:00:32 -0400 From: Miguel Howard <mig...@jmol.org> Subject: Re: [Jmol-developers] Java 1.5 To: jmol-developers@lists.sourceforge.net Message-ID: <o2vab20ac2d1004281300g11e7aa92pb730a4383c638...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 On Tue, Apr 27, 2010 at 5:17 PM, Robert Hanson <hans...@stolaf.edu> wrote: > Does it matter that Jmol 12 will require Java 1.5? Java 1.5 was released in Sept 2004 Requiring 1.5 should not be an issue for anyone. Miguel ------------------------------ Message: 7 Date: Wed, 28 Apr 2010 17:08:59 -0500 From: Robert Hanson <hans...@stolaf.edu> Subject: Re: [Jmol-developers] 2D/3D project To: jmol-developers@lists.sourceforge.net Message-ID: <v2iba9c0bd61004281508j7ec9f399i1683e7d25e395...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" 2010/4/28 Angel Herr?ez <angel.herr...@uah.es> > I've been playing for somewhat long time with connecting JChemPaint for 2D > drawing toJmol > for 3D rendering. > It's over a year that I have a working prototype, but haven't released it > public because I was > expecting to polish it up. In fact, that's the topic of one of my > presentations at BCCE next > August in Denton. > > A few bugs or lack of features in the Javascript API of JChemPaint have > refrained my > progress with this. Then, JCP v3 was started with quite a reworked engine, > and I posed great > expectation on it, but haven't been able to solve my pending issues with > this new version, so > I'm still relying on the old v2. Particularly, addition of explicit > hydrogens has been a constant > problem. And Jmol minimization heavily depended on the Hs being present in > order to be > successful. So what I have is a semimanual procedure which is not too > user-friendly. > I haven't yet had the chance to explore the recent addition in Jmol of > calculate hydrogens, > which may solve my bottleneck with JCP. > Now, of course, Jmol can add its own H atoms. That's what minimize addHydrogens does > > I have therefore followed -but couldn't keep pace with- the recent and so > very fast > developments in connecting JME with Jmol, with excitement but also with a > bit of dismay at > having lost my chance to be "the first" ;-) Great work, Otis and Bob! > > My bet for JCP was based, of course, on it being open source. I guess the > connection could > be done at the Java level but my knowldege limited me to using Javascript. > > I'm MORE than happy to work with something that is already out there. Mostly interested in developing the 2D->3D and want something that is open source - and adaptable :) > > > > ------------------------------------------------------------------------------ > _______________________________________________ > Jmol-developers mailing list > Jmol-developers@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ ------------------------------------------------------------------------------ ------------------------------ _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers End of Jmol-developers Digest, Vol 47, Issue 6 ********************************************** ------------------------------------------------------------------------------ _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
