Ewen, this is much appreciated. All you have to do is fill out a feature request, and who knows? You may be done with Chime before you know it. So please take a moment and fill in one request per distinct feature at http://sourceforge.net/tracker/?group_id=23629&atid=379136
I had never heard of Chime's Sculpt mode, but if it's anything like Jmol's "draw" mode, where you can move arrows and axes and planes and such around in space -- but with atoms -- this is certainly a possibility. Right now using JavaScript you can move atoms; doing this with a mouse should not be a big deal. I'd like to hear more about Scuplt mode. How does it work? (From the user's perspective.) I think part of what you are seeing is a response to what is at http://en.wikipedia.org/wiki/MDL_Chime: "Calculating and drawing molecular surfaces coloured according to electrostatic or hydrophobic potential. Chime can calculate these surfaces for any molecule." This is a BIT of an exageration. Chime has no magical powers. When you give Chime a set of coordinates, this is in no way sufficient information to "calculate a molecular surface according to electrostatic potential." Although the Chime programmers are sworn to secrecy, I have come to the conclusion that whatever they do in this regard is a convenient fake. Something that looks OK, but isn't in any way "according to the electrostatic potiential" -- at least not any generally accepted potential. They are faking the charges on atoms, probably using simplistic electronegativity ideas. Egon and others in the Steinbeck group at CUBIC in Cologne, Germany, and I had an extensive discussion on this back in August, and we concluded that the proper quantum mechanical calculation of charges is beyond the scope of even Jmol. So our solution is to render any electrostatic potential for any molecule for which charge data are provided. This includes an ever-widening range of formats from a number of calculational programs. If anyone finds a file format with charge data that are not being read, all they have to do is ask, and the charges will be there the next time around. As for lipophilic surfaces -- does anyone know how to calculate this? If it's simple, we can just plug it in to Jmol as another isosurface option. Bob Hanson Ewen McLaughlin wrote: >That 'someone' would be me. I wouldn't say I was 'miffed' about the lack >of Sculpt in Jmol; just disappointed. I tried to make the Jmol and Chime >articles factually correct and unbiased. They claimed that Jmol had >superseded Chime and that Jmol had all the features of Chime. The first >statement was unsupported and the second is untrue. > >I really appreciate the effort that has gone into Jmol and look forward >to changing from Chime - but I can't yet because Jmol does not have all >the features I use. > >Ewen McLaughlin >Lecturer in Chemistry >Swansea College > >-----Original Message----- >From: [EMAIL PROTECTED] >[mailto:[EMAIL PROTECTED] On Behalf Of Phillip >Barak >Sent: 29 September 2006 21:18 >To: [EMAIL PROTECTED]; [email protected] >Subject: Re: [Jmol-users] Jmol in Wikipedia > >Interested parties might also visit the >http://en.wikipedia.org/wiki/Talk:MDL_Chime to see the dispute over the >statement that "Chime has been largely superceded by Jmol..." >Apparently, someone particularly enamored of the Sculpt mode of Chime, >and miffed that the Jmol community has not yet picked up his feature >request, has picked up the cudgels for Chime. > >----- Original Message ----- >From: Nicolas Vervelle <[EMAIL PROTECTED]> >Date: Friday, September 29, 2006 2:27 pm >Subject: [Jmol-users] Jmol in Wikipedia >To: Jmol Users <[email protected]> > > > >>Hi Jmol users, >> >>I am starting to have a discussion on Wikipedia about Jmol compared >>to >>Chime. >>http://en.wikipedia.org/wiki/Talk:Jmol >> >>Everyone is invited to participate to make the article true and not >>biased. >>Nico >> >> >>-------------------------------------------------------------------- >>----- >>Take Surveys. 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Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share >your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDE >V >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > >Swansea College >Tycoch Road, Tycoch, Swansea. SA2 9EB >website: http://www.swancoll.ac.uk >****************************************************************************************************************************************** >The information contained in this message is intended for the addressee only >and may contain confidential and/or >privileged information. 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