Bob and Martin, I've asked Bob before about Jmol and Chime and the apparent ability of Chime to calculate MEP surfaces. He's consistently and fairly argued that this is not something Jmol should encompass. This disappointed me because I use Chime MEP surfaces for teaching basic ideas about molecular polarity, but it's not a lightly-taken decision.
I've converted my old Chime resources into Jmol ones now, except the ones using MEP surfaces (and the dreaded Sculpt mode). Wanting to push on with my Chime --> Jmol conversions, I have a newbie question for Bob: What software would you use to calculate the MEP surface properly from a mol (or other) file? Ewen PS Sorry if I missed it Bob, but did anything happen with lipophilic potential colouring of surfaces? -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bob Hanson Sent: 02 May 2007 17:02 To: [email protected] Subject: Re: [Jmol-users] Requesting electrostatic potential with Rasmol coloring scheme for MOL and CML files Martin Slavík wrote: >In Jmol I really miss displaying electrostatic potential with /Rasmol/ >coloring scheme (it is usefull for depicting small variances in partial >charges and handy for educational purposes) for every file type. > I'm not certain what that coloring scheme is, but it's possible that you aren't taking full advantage of the isosurface command. You can set the range of colors to whatever you want, and there are five or six color schemes. Can you be more specific -- a specific file, perhaps? > In >Chime there was a possibility to display electrostatic potential for >every file type (eg. MOL), nowdays in Jmol we can display it only for >certain file types. > No one will tell us what secret the Chime developers used to fake charge distributions. So we made the decision this past summer to not have Jmol do that and instead allow for any file type that has charge data in it already to be displayed. It's a slightly different philosophy. But there are many file types now that are supported, and if you have another, I can do that in a day. > In addition, for files without appropriate data >(MOL, CML), label %P displays partial charge=0 instead of -- or some >approximation (as in Accelrys ViewerLite). > > > Again, Jmol is not going to get into the approximation business in this regard. I think as a web page developer you just have to know what files you are working with and choose file types that are appropriate. Then you won't have this problem. >I will enjoy to have possibility to display such rough approximation >(electrostatic potential with /Rasmol/ coloring scheme) and/or label for >partial charge for files without appropriate data. > > Not going to happen, sorry. That decision is final - we need the appropriate data. Partially this is so that we can say that when you look at a rendering of MEP in Jmol it reflects what the calculation intended, not some crude approximation invented by me. That's one difference between Jmol and Chime. Is there a reason you can't have control over using the %P label option only when appropriate? Bob ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users Swansea College Tycoch Road, Tycoch, Swansea. SA2 9EB Coleg Abertawe Heol Tycoch, Tycoch, Abertawe. SA2 9EB website/wefan: 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. If you are not the addressee, please delete this message and notify the sender; you should not copy or distribute this message or disclose its contents to anyone without the express permission of the author who is the copyright holder. Mae’r wybodaeth yn y neges hon wedi’i bwriadu ar gyfer y derbynnydd yn unig a gall gynnwys gwybodaeth gyfrinachol a/neu freintiedig. Os nad chi yw’r derbynnydd, dilëwch y neges hon a rhowch wybod i’r anfonwr; ni ddylech gopïo neu ddosbarthu’r neges hon neu ddatgelu ei chynnwys i unrhyw un heb ganiatâd penodol yr awdur sy’n ddeiliad hawlfraint. ********************************************************************* ********************************************************************* ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
