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Re: [Jmol-users] Re : Re: color a surface according to distance from a selection
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From: Bob H. <ha...@st...> - 2007-11-22 18:13:34
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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 pau...@ac... 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 <ha...@st...> >Date: Mercredi, Novembre 21, 2007 8:37 pm >Objet: Re: [Jmol-users] color a surface according to distance from a selection >À: jmo...@li... > > > >>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 >> >> >> >> >>pau...@ac... 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 >>>Jmo...@li... >>>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 >>Jmo...@li... >>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 >Jmo...@li... >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 |