Rajarshi wrote: >> As I said before, I don't understand why biotech/pharma professionals >> need a browser tool. >> >> If they do, then I would love to talk to them. > > OK - I'm currently a grad student who will (hopefully) become a > professional in the near future.
I hope so too :-) > For me Jmol is a very useful piece of software as its focus is on > visualization. > Since the comparison with PyMOL has come up I would say that when I want > to do > manipulations and processing of molecules and molecular information I > would > turn to something like PyMOL (or MOE) - which are 'environments' for > handling molecules. > > But as Warren has mentioned, PyMOL and its ilk are multi function, large > footprint tools. > > When all I want is to look at a structure(s) Jmol is fills the niche > perfectly. OK > One use of Jmol for me has been to use it to view molecules in an > environment > which is not oriented towards chemistry. > Specifically when I do statistics in > R, it is sometimes handy for me to be able to view a structure quickly. > Previously I would have to keep a Hyperchem window open in VMWare or else > keep > PyMOL open and so on. But the fact that Jmol is java based allows me to > integrate it into my workflow quite easily. > > I think thats where Jmol shines - its a 'component' and not a full blown > application. Good. That is what I think it is supposed to be. > I'm surprised that you mention that Jmol is regarded as > something for novices and toy-like. I don't recall anyone waying that it is 'toy-like' My comments about 'novices' refer to the fact that this is the group of people that I am trying to reach. My personal motivation for working on Jmol is to provide a web browser tool so that educators can teach their students. The professionals and researchers have software tools. Professionals pay serious money for a lot of them, so I assume that they must be happy and well-served. The corporations do no pay any money to support me or Jmol (despite my requests), so I assume that they are not interested. It seems that the educators (and their students) get nothing more than a few table scraps. > I think it does what its meant to do very well! Good. > I agree that it is missing certain functionality - but I see no reason why > they > cannot be included over time bringing Jmol upto the 'professional' level. But that should be *your* job, and the job of the professional chemists, not my job. I am a computer scientist, not a chemist. > I realize that you shoulder the main load of maintanence > & development - but I believe that the Jmol community is > a huge asset and I am certainly willing to help with > whatever I can - which is mainly comments and testing > right now due to time constraints. I truly appreicate your help. But the unfortunate fact is, I feel that I have had to learn a *huge* amount of chemistry, much more than was appropriate. Everyone would be better off if there were some serious chemists working on Jmol. That way I could spend more time on architecture, packaging, code review, and project management rather than learning and implementing details within the Chemistry application space. It is incredibly inefficient for me to learn about and try to understand chemical/biochemical/crystallographic concepts via email. > The only reason why I think that Jmol might not be > the focus in a professional enviroment is that those > environments are already working with tools that > carry out visualization (say PyMOL / MOE etc). Exactly > In that case its understandable that > they would not introduce a new tool. > However a I mentioned above, if you > look at Jmol as a component then I think that > is an important and useful peice of software. I certainly hope that it is a useful component. Miguel ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://productguide.itmanagersjournal.com/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
