Talk:MDL Chime

Talk

1. ^ On 26/9/06 Google listed about 45,000 hits for JMol molecular graphics versus 75,000 for Chime molecular graphics.

2. ^ JMol does not have a Sculpt mode, for example.

15:14, 26 September 2006 194.81.161.150 15:09, 26 September 2006 194.81.161.150

I've moved the notes from 194.81.161.150 to this talk pg, and reverted. Original research is generally frowned upon in wikipedia; further, the relevance of Google hits to the issue at hand is hard to see. A Chime user must download a Chime plugin once and then need never search on the Chime term again. A Jmol user need never have gone even that far, since the Java applet just silently downloads from the source page. Google 'hits' (on a given day?) just doesn't strike me as very firm evidence of anything...might be interesting to see a couple of yr trend, though. On the other hand, the jmol-users listserve that I monitor is mainly populated by former Chime developers. The point about the Sculpt mode is valid, though rather difficult to fathom its significance without first adding a description of the Sculpt mode to the Chime article. PBarak 01:43, 27 September 2006 (UTC)

It's a bit hypocritical to criticise the 'original research' I gave on the relative popularity of chime to Jmol and then justify the otherwise unsupported assertion that 'Jmol has largely superseded chime' by using an impression you gained from following jmol discussion groups. Besides, chime is no longer being developed, so it's not surprising to find chime developers looking for something else to do...

The google hits seemed to be for websites that used molecular graphics embedded using either chime of jmol. Looks to me like jmol is used on 60 % of the number of sites using chime.

I use chime for teaching. Sculpt mode is great for illustrating cis/trans isomerism. Chime can also estimate electrostatic potential surfaces which is fantastic for illustrating molecular polarity. Jmol can't do that! I've asked the developers of jmol to include these features but they seem more interested pursuing their own ends - mostly to do with graduate-level work, it seems to me.

Ewen 05:52, 28 September 2006 (UTC)

Hmmm, my impression from following the jmol discussion groups....probably wouldn't move you from your point of view.

How very cynical of you. Nice to see you assuming the best of people ;-) Ewen 21:52, 29 September 2006 (UTC)

I believe that it was you who started out your with "it's a bit hypocritical..." and you appeared to assume that I followed only the jmol groups and hence could not make an informed comparison. I think that you also implied that Chime developers have nothing better to do than to develop Jmol(!), but that's alright too. Enjoy. PBarak 23:01, 29 September 2006 (UTC)

Well someone wasn't making an 'informed comparison' because they wrote that Jmol had superseded Chime; which struck me as more like wishful thinking than anything clearly established by any evidence. Evidence from the discussion lists was interesting, but since Chime hasn't moved on since 1998 and Jmol is in active development I reckon that much activity on the Jmol list can be attributed to that, rather than to the relative popularity of the two prgrammes. Ewen 06:57, 30 September 2006 (UTC)

Have a look yourself at usage stats for jmol-users and jmol-developers (at sourceforge.net) on one hand and molvis-list on the other, which I've monitored from 1998 (when it was the RasMol list) to the present. (The Molvis-list is for discussion of molecular visualization software, especially free software and its uses in education, such as MDL Chime, Protein Explorer, and RasMol.) Molvis was down to 0.36 messages a day in 2005; less in 2006. Eric Martz, a leader in the development of Chime resources, recently wrote: "I suspect that the dizzying level of traffic on the jmol-users list, and the well-justified excitement about Jmol, has diverted some traffic from molvis-list. I myself am working more and more with Jmol." PBarak 20:13, 29 September 2006 (UTC)

Well, that's great. I honestly hope that Jmol succeeds in replacing Chime, but it doesn't do it for me yet. My thought on reading the Chime and Jmol entries here was that the statements about Jmol superseding Chime were without evidence and, I suspect, untrue. Yes, Jmol is generating a lot of excitement but there still seem be more chime sites than jmol. Wikipedia is not the place to advertise one product to the detriment of another, even if it is worthy and exciting. Ewen 21:52, 29 September 2006 (UTC)

in my opinion, three of the most important benefits of Jmol over Chime are 1) platform compatibility, 2) applet and application, and 3) it is open-source. Chime is severely limited regarding point 1; essentially it runs under Windows. Jmol runs under Windows, OS X, Linux, and other OS. also, Jmol is distributed as an applet and an application, making it a more flexible software tool. finally, and most important in my opinion, Jmol is open-source. anyone with Java experience can add their own features, build other applicaitons on top of Jmol, etc. in addition, the Jmol license expressly allows commercialization of Jmol-derived products (as long as the Jmol core remains open). if you think it is difficult to persuade Jmol developers to do what you want, you have no idea what is was like trying to persuade MDL even to fix well-documented and long-standing bugs! to say nothing of actually adding features - that was accomplished 'on the sly' as near as I can tell. Chime was an excellent tool. it had a number of powerful features that Jmol thus far lacks - energy minimization for one, and IR spectra. surfaces are still in their infancy in Jmol. but the reverse is also quite true. animating is much easier in Jmol. Jmol handles crystal lattices. you can draw shapes in Jmol. labeling and captions are much more flexible. you can export to ray-tracing programs. you can export 2D images. you can access a huge amount of information about the structure in Jmol, without resorting to callbacks. and that is a very short list, from my fairly limited perspective as a developer of educational resources. while I respect Chime and MDL for what they had a hand in starting (3D mol vis via the Web), I can't help but feel frustrated that they apparently abandoned the education aspect of it. -tim d 204.111.135.109 03:41, 30 September 2006 (UTC)

I totally agree! It's a pity that I'm still stuck with Chime due to its energy minimisation ('sculpt') feature. As soon as Jmol reproduces that feature I'll swap. I only wish that before putting in the effort of developing the many impressive features you list for Jmol, that Jmol had reproduced all Chime's features. Perhaps I'm refusing a gift Ferrari because I want a car which isn't red... 8-)

Ewen 06:57, 30 September 2006 (UTC)

Ewen, if you want a specific feature added to Jmol, I recommend submitting a feature request at the project page [[1]]. browsing all open requests, I see nothing related to Sculpt mode, which may explain why it has not been addressed by any developers. <shrug> as for reproducing all of Chime's features, well, development of Jmol has followed the direction of its users. it has a different, perhaps wider, user base compared to Chime, so it is no wonder the two are different in some respects. I doubt Jmol will ever reproduce all of Chime's features because it is user-driven and not corporate sponsored. some things in Chime just are not as useful to the community as a whole. but I do suggest that you submit a feature request for your particular feature. regards, tim d 204.111.135.109 01:59, 2 October 2006 (UTC)

OK, I've put in a formal request. I did raise the issue with the Jmol users group (31-3-04). I appreciate that it might be a minority request and require much work. Ewen 09:44, 2 October 2006 (UTC)