tag:blogger.com,1999:blog-6701417360427959244.post4537027003640002893..comments2024-03-27T07:18:00.323+01:00Comments on Molecular Modeling Basics: ChemDoodle Web Components: 2D to 3D and MolGrabberJan Jensenhttp://www.blogger.com/profile/08595894308946022740noreply@blogger.comBlogger10125tag:blogger.com,1999:blog-6701417360427959244.post-36370667829019778312011-03-18T07:35:30.971+01:002011-03-18T07:35:30.971+01:00That's right. Under the Tools menu. Here is ...That's right. Under the Tools menu. Here is <a href="http://www.chemaxon.com/marvin/sketch/index.jsp" rel="nofollow">a link to MarvinSketch</a>. See <a href="http://molecularmodelingbasics.blogspot.com/2009/08/building-complicated-molecule-meet.html" rel="nofollow">MarvinSketch in action on MMB</a>.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-30632564966869738442011-03-17T18:29:22.242+01:002011-03-17T18:29:22.242+01:00There is also a structure-to-name feature availabl...There is also a structure-to-name feature available in MarvinSketch (which is free).Anonymoushttps://www.blogger.com/profile/18123073028209991396noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-60404486803026981532011-03-16T02:27:42.993+01:002011-03-16T02:27:42.993+01:00Hi Geoff,
I very much look forward to continuing ...Hi Geoff,<br /><br />I very much look forward to continuing our discussions. I was very happy to see this post from Jan, as I am a fan of Avogadro and am also eagerly awaiting the 1.1 update. I think all open-source projects benefit from each other and I believe Avogadro and the ChemDoodle Web Components are complementary technologies. We should talk more about this; I will send you another email.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-82114448490633136742011-03-15T15:17:43.022+01:002011-03-15T15:17:43.022+01:00@kevin,
I think the ChemDoodle desktop and web co...@kevin,<br /><br />I think the ChemDoodle desktop and web components are great -- as you know, I use them myself. I mostly wanted to remind Jan that for this particular use, there's an easier way.<br /><br />I think the NMR and MS simulation is great. I might add that to Avogadro for my own personal use.Geoff Hutchisonhttps://www.blogger.com/profile/12183565052523203480noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-47057333815788437972011-03-14T22:04:14.166+01:002011-03-14T22:04:14.166+01:00I'm glad Harm brought that up. ChemDoodle desk...I'm glad Harm brought that up. <a href="http://www.chemdoodle.com" rel="nofollow">ChemDoodle desktop</a> provides even more features than the competition and the entire ChemDoodle desktop API is accessible through the ChemDoodle Web Components library.<br /><br />For instance, an instructor can <a href="http://web.chemdoodle.com/demos/simulate-nmr-and-ms" rel="nofollow">simulate NMR and MS</a> with the web components. This works on iPads too!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-51863660631749141602011-03-14T15:03:07.614+01:002011-03-14T15:03:07.614+01:00Commercial solutions are definitely welcome, so th...Commercial solutions are definitely welcome, so thanks! They are just harder to use in teaching because students don't have access to them,at least at home.<br /><br />However, they serve as great inspiration for new features in free programs.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-30500078161283299462011-03-14T14:49:58.562+01:002011-03-14T14:49:58.562+01:00I don't know if commercial solutions are welco...I don't know if commercial solutions are welcome here, but ChemBioDraw has advanced structure-to-name, structure to NMR (for small organic molecules) and some more useful functions. Just to add to the boiling soup of knowledge here...harm82https://www.blogger.com/profile/01769139395621125447noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-66624698766441927242011-03-14T08:23:06.405+01:002011-03-14T08:23:06.405+01:00That is much easier! No argument there. Yes, I th...That <i>is</i> much easier! No argument there. Yes, I think a great feature like that deserves to be made more prominent. Like an icon on the tool bar!<br /><br />A structure-to-name feature would be great! Is there an ETA on Avogadro 1.1?Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-75560711115779017912011-03-13T23:52:13.428+01:002011-03-13T23:52:13.428+01:00I was just about to say, I already added that to A...I was just about to say, I already added that to Avogadro - maybe it needs to be more prominent? It is a great feature, fetch by chemical name, modify, generate input file, run, analyse.Marcus D. Hanwellhttps://www.blogger.com/profile/08187423171219662136noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-41045066563597911312011-03-13T17:05:41.764+01:002011-03-13T17:05:41.764+01:00Actually, there is an easier way to go from a name...Actually, there <b>is</b> an easier way to go from a name like "aspirin" to a 3D structure in Avogadro. It's built in. :-)<br /><br />Go to the File menu: File -> Import -> Fetch by chemical name<br /><br />This will search PubChem and use the NIH Chemical Resolver to generate a 3D structure.<br /><br />Avogadro 1.1 will have an even better way to learn nomenclature -- it will use the Chemical Resolver to generate IUPAC names for most standard structures.Geoff Hutchisonhttps://www.blogger.com/profile/12183565052523203480noreply@blogger.com