Talk:Jmol

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Chime[edit]

I'm not disputing that JMol is good, developing well and, as open-source, has the moral high ground over chime. It's just that Chime can do stuff that JMol can't.

Ewen 15:21, 26 September 2006 (UTC)

It's Jmol, not JMol. Specifically, what stuff ? A lot of new features are being added (surfaces, ...)
Thanks NicoV. I see, just like me, you forget to sign your comments!
Jmol, JMol. It makes a difference? Whatever..
Yes, it makes a difference: JMol is an existing other free program. Jmol team had remarks from the JMol author to clearly make the distinction. NicoV 19:30, 28 September 2006 (UTC)
Chime's 'Sculpt' mode and its ability to create electrostatic and hydrophobic surfaces are important to me as a high school teacher. As far as I know, Jmol is not planned to include these features. I would honestly like to use Jmol instead of chime but until it does what chime can do - everything chime can do - I'm not impressed by the features which are more advanced than chime. They seem designed for postgraduates rather than more basic chemists.
Ewen 10:24, 28 September 2006 (UTC)
I am not a chemist, so I may be wrong but Jmol can compute MEP surfaces. Isn't it what you're talking about ? NicoV 19:30, 28 September 2006 (UTC)
It might be - I've not seen it done and I've had a good look at Jmol. I'll look again and ask around. Sculpt mode is still a killer app for Chime, as far as I'm concerned. Ewen 05:45, 29 September 2006 (UTC)
That's one of the many features added in the last weeks / months. Check the prereleases. And, BTW, I don't think Wikipedia is here to make comparisons. -- NicoV 17:39, 29 September 2006 (UTC)
I checked http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/isosurface.htm and it's clear that although Jmol v11 can draw MEP surfaces, it needs partial charge data to do so. Chime can calculate the partial charges for any molecule loaded, so Jmol still has to catch up. Ewen 13:52, 1 October 2006 (UTC)
I appreciate your enthusiam. As far as I know calculating basic partial charges are not an issue at all, see BO algorithm dictionary. I recommend to contact any of the BO member mailing lists, e.g. Jmol, or the BO mailing list directly, since I have the same opinion like Nico. Wikipedia should not be a feature discussion forum for Jmol. This is a reason why projects have mailing lists, feature tracking and bug tracking systems. JKW 15:46, 1 October 2006 (UTC)
I look forward to Jmol superseding Chime. The current version of chime still has two features that jmol has not. you say that this will soon be down to one feature - good, but not yet enough for my purposes. Sorry guys; I know you're working hard on it.
If wikipedia isn't to make comparisons, should we remove all reference to chime on the jmol page and vice versa? I think comparison of the two programs is relevant and necessary; wikipedia ought to be unbiased, that's all. When I came across the jmol article it asserted that jmol had superseded chime: That's not only a comparison, but an untrue one.
Ewen 18:14, 29 September 2006 (UTC)
I don't say that it will be down to one feature, I am saying that MEP is already available in Jmol (10.9.x). I would remove the assertion that Jmol has superseded Chime, this is a biased POV. But, if you want to make comparison, make it unbiased, that is compare them completely, not just by saying that one feature is not available: Chime has features that Jmol doesn't have, and Jmol has features that Chime doesn't have -- NicoV 20:27, 29 September 2006 (UTC)
I believe you! Not being a Jmol user I'm not in a position to list features of Jmol which Chime does not have. I have tried to correct untrue/unverified statements such as 'Jmol has all the features of Chime' and 'Jmol has superseded Chime'. I've added what I know, which is mostly about Chime. Ewen 11:34, 30 September 2006 (UTC)
Sorry folks, but this fight over whether who is superseding whom comes over as a bit childish. Even when supported with numbers from some (arbitrary) Google searches. That can never be neutral nor objective. Why not restrict yourselves to saying that Jmol aims to offer all the functionality of Chime to become an open replacement? The decision whether to actually replace or not can only be left to the individual user. Throw out the subjective claims, the Google search, and the discussion about one particular feature as pseudo-proof of any claims. (I can see the value of Sculpt for teaching, but just as not everyone is a post-graduate, not everyone is a teacher either.)
One final swipe: I cannot understand how you start a debate on this while not correcting a plain grammatical error in the very first sentence of the article: "Jmol is molecule viewer ...". I'll make some minor language changes now. For the record, I write as a Jmol sympathiser and Jmol-users subscriber. SeL 13:18, 30 September 2006 (UTC)
And an afterthought: there is nothing wrong with including a more thorough feature comparison, but don't do it to try and prove any point: try to be informative to support users in their independent, case by case decisions. SeL
I agree completely, this dicussion is useless, since Jmol and Chime are by far not the only software products on the market. If you really want to contribute create a page like List of molecular modelling software, and Comparison of molecular modelling software, and include some other tools like PyMOL, ICM-Browser, Ghemical, BALLView, and also full suites like Maestro, Discovery Studio, ICM Pro, InsightII, Sybyl, etc.. If you do not know where to start have e.g. a look at List of wiki software, Comparison of wiki software. JKW 14:11, 30 September 2006 (UTC)
Darn you! I'm outed as a childish mol-vis dilettante. Fair enough! I rather approve of the current page, though. Accurate and unbiased. 8-) Ewen 19:53, 30 September 2006 (UTC)

I used to use Chime extensively, up to the point where Chime support for the Mac and for Linux was discontinued. Currently, to run Chime on a Mac, I have to use the Classic environment and Netscape 4.x. In a university environment where every student is free to use whatever type of Computer she or he likes, I generally give preferrence to programs that are available equally for MacOSX, Linux and Windows, and I refuse to produce Webpages that are not as platform-independent as I can make them. Chime Webpages simply do not work on current browsers outside the Windows environment. Therefore, despite all its nice features, to my frustration Chime became unusable to me even before I found out about Jmol. While not all features of Chime are (yet) available in Jmol, I am very impressed with the speed with which new features are incorporated in Jmol, and with the speed with which my own suggestions to the developpers of Jmol have been incorporated. The problem with determining the uage of Jmol is that its name is a lousy search term, as the web is full of Jmol as an abbreviation of Joules x Mol related to calculation of energies and a abbreviation of "journal of molecular something or other", of which there are many around. This problem makes it very difficult to determine the true abundance of Jmol-pages on the web. Ahonegger 07:00, 2 October 2006 (UTC)

Derivation[edit]

From the perspective of someone with absolutely no familiarity with this subject, I assumed "JMOL" was an acronym, but couldn't figure out how the name was derived. After sniffing around various links, I'm guessing it's (J)ava + (.mol) (as in "Molfile",) apparently the term for a metadata file relating to a molecule.

Perhaps this could be clarified, e.g.:

Jmol ((J)ava + (.mol) is an open-source Java viewer for chemical structures in 3D[1]. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research in chemistry and biochemistry...

Caen (talk) 10:56, 13 February 2008 (UTC)

  1. ^ [How to cite Jmol|http://jmol.sourceforge.net/#How%20to%20cite%20Jmol]