Well, thanks Bob. As I had limited access to the internet I only tried with the already released version ;-) 11.3.43 and it worked beautifully ! I am glad to have been ahead of you during 5 minutes, but I am certain that I do not deserve it ! Cheers, Paul
----- Message d'origine ----- De: Bob Hanson <[EMAIL PROTECTED]> Date: Jeudi, Novembre 22, 2007 7:32 pm Objet: Re: [Jmol-users] Re : Re: color a surface according to distance from a selection À: [email protected] > Yes, provided you are using the unreleased build of Jmol 11.3.47 > currently in http://chemapps.stolaf.edu/jmol/docs/examples-11 > > > OK, this is a bit in flux. Jmol 11.2 uses > > select whatever; calculate surface > > specifically for the purpose of calculating the "shrink-wrap" > surface around a molecule. The idea there is that all the > (significant) atoms are within the wrap. Solvent might be excluded, > for example, by not selecting it. > > Paul's request is for something else -- a distance from a ligand to > somewhere else outside that volume. That is not possible in Jmol > 11.2, but I just implemented it in Jmol 11.3.46 and 11.3.47. > > When I responded below to Paul, I didn't realize that 11.2 couldn't > do this using calculate surface. Paul, you are ahead of me, because > > calculate surfaceDistance > > is precisely my second idea, what you want to use in Jmol 11.3.47 > > Here's how to do it in 11.3.46: > > calculate surface {whatever} > > That works in 11.3.47, too, but I'm deprecating "calculate surface" > because of the possible confusion there with these two applications > in favor of > > calculate surfaceDistance FROM {whatever} > calculate surfaceDistance WITHIN {whatever} > > which seems to me much more clear, since you really are just > calculating the surfaceDistance property, not a real "surface". > > The plan is to make > > select whatever; calculate surface > > default to > > calculate surfaceDistance WITHIN {whatever} > > to remain compatible with 11.2, but > > select whatever; calculate surfaceDistance > > default to > > calculate surfaceDistance FROM {whatever} > > because that seems more natural and is what Paul would use. > > In any case, the more explicit forms would be preferred and > documented. > > Bob > > > [EMAIL PROTECTED] wrote: > > >Hi Bob and thank-you for your answer ! > >I assume that in #1 it should read "select whatever; calculate > surfaceDistance" ? > >Paul > > > >----- Message d'origine ----- > >De: Bob Hanson <[EMAIL PROTECTED]> > >Date: Mercredi, Novembre 21, 2007 8:37 pm > >Objet: Re: [Jmol-users] color a surface according to distance from > a selection>À: [email protected] > > > > > > > >>PAUL, this is possible, and with Jmol 11.3.46 it will be > >>especially good. > >> > >># 1: create the surfaceDistance property values > >> > >>select whatever; calculate surface > >> > >># 2: create the isosurface > >> > >>isosurface select(someAtoms) ignore(whatever) sasurface /* or > >>MOLECULAR > >>*/ map property surfaceDistance > >> > >> > >>In the current version of Jmol, this produces sort of a patchy > >>isosurface, because the color of any piece of the isosurface due > >>to a > >>given atom is based on just that atom's property value. In Jmol > >>11.3.46 > >>this will be much smoother. The patchy look can be created if > >>desired using > >> > >> set isosurfacePropertySmoothing false > >> > >> > >> > >>Bob > >> > >> > >> > >> > >>[EMAIL PROTECTED] wrote: > >> > >> > >>>Hello Jmolers, > >>>I would like to know if there is a way to color an isosurface > >>> > >>> > >>with a gradient mapping the distance from the different vertex to > >>the selection set. There is a similar function in chime which > >>allows to emphasize the contacts between two chains (contact > >>surface in protein explorer). > >> > >> > >>>My aim is to show the contacts between an antibody and an antigen. > >>>Thanks in advance if you have any clue for doing that. > >>>Paul > >>> > >>>----------------------------------------------------------------- > >>> > >>> > >>-------- > >> > >> > >>>This SF.net email is sponsored by: Microsoft > >>>Defy all challenges. Microsoft(R) Visual Studio 2005. > >>>http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >>>_______________________________________________ > >>>Jmol-users mailing list > >>>[email protected] > >>>https://lists.sourceforge.net/lists/listinfo/jmol-users > >>> > >>> > >>> > >>------------------------------------------------------------------ > - > >>------ > >>This SF.net email is sponsored by: Microsoft > >>Defy all challenges. Microsoft(R) Visual Studio 2005. > >>http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >>_______________________________________________ > >>Jmol-users mailing list > >>[email protected] > >>https://lists.sourceforge.net/lists/listinfo/jmol-users > >> > >> > >> > > > >------------------------------------------------------------------- > ------ > >This SF.net email is sponsored by: Microsoft > >Defy all challenges. Microsoft(R) Visual Studio 2005. > >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >_______________________________________________ > >Jmol-users mailing list > >[email protected] > >https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > -------------------------------------------------------------------- > ----- > This SF.net email is sponsored by: Microsoft > Defy all challenges. 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