On Wed, Sep 14, 2011 at 1:29 PM, nsmith Clemson <[email protected]>wrote:
> Well, how is the functionxyz supposed to be used? What is the ideal > scenario for it? I haven't found any well-done examples after a couple > google searches. > > FunctionXyz assigns values throughout a 3-dimensional grid of points in x, y, and z. It is equivalent to a "cube" file. Then one selects a cut-off value, and Jmol draws the best surface it can create through that block of points based on those values. > On Sep 14, 2011, at 2:12 PM, Robert Hanson <[email protected]> wrote: > > There might be easier ways to do this than functions, then. spheres are > simple; cones are basically simple functions; parallelpipeds are just > planes. So I think the only function you need there is for the cones. > Something like this: > > isosurface cone1 color gray color translucent 5 functionxy = > "-0.71*(x**2+y**2)**.5" > > > > On Wed, Sep 14, 2011 at 12:43 PM, Nicholas Smith < <[email protected]> > [email protected]> wrote: > >> I am planning on using the applet and will be attempting to generate >> fairly "standard" objects such as spheres, cones, parallelepipeds, etc. >> Mostly geometric objects. It should not be a completely irregular object. >> >> >> On Wed, Sep 14, 2011 at 1:20 PM, Robert Hanson < <[email protected]> >> [email protected]> wrote: >> >>> I realize there is not a lot there on that, and some of it has recently >>> changed. >>> >>> Q: Are you planning to use the applet or the application? >>> Q: Will this be fairly "standard" functions, or something you definitely >>> need to generate yourself? >>> >>> On Wed, Sep 14, 2011 at 12:09 PM, Nicholas Smith <<[email protected]> >>> [email protected]> wrote: >>> >>>> Hello, >>>> >>>> I'm fairly new to Jmol and have been tinkering with methods of inserting >>>> isosurfaces into protein space. I've been looking into the documentation >>>> for >>>> the functionXY and functionXYZ isosurface options and was wondering how to >>>> accomplish a couple things: >>>> >>>> functionXYZ: >>>> What sort of data should I fill in the returned array with? (the >>>> fxyz[ni][nj][nk]) >>>> Is it a potential map of sorts? What is it? >>>> >>>> functionXY: >>>> I messed around with mainly the ni, nj, and nk arguments, and the >>>> maximum values passed in for each argument is an 11. Is there a way to >>>> increase the grid space that the function is graphed over, or is this the >>>> maximum distance? >>>> >>>> This is the documentation I've been going off of: >>>> <http://chemapps.stolaf.edu/jmol/docs/#isosurface> >>>> http://chemapps.stolaf.edu/jmol/docs/#isosurface >>>> If there's a better source let me know. >>>> >>>> I would appreciate any suggestions, >>>> Nick Smith >>>> >>>> ------------------------------------------------------------------------------ >>>> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA >>>> Learn about the latest advances in developing for the >>>> BlackBerry® mobile platform with sessions, labs & more. >>>> See new tools and technologies. Register for BlackBerry® DevCon >>>> today! >>>> <http://p.sf.net/sfu/rim-devcon-copy1> >>>> http://p.sf.net/sfu/rim-devcon-copy1 >>>> _______________________________________________ >>>> Jmol-users mailing list >>>> <[email protected]>[email protected] >>>> <https://lists.sourceforge.net/lists/listinfo/jmol-users> >>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>>> >>> >>> >>> -- >>> Robert M. Hanson >>> Professor of Chemistry >>> St. Olaf College >>> 1520 St. Olaf Ave. >>> Northfield, MN 55057 >>> <http://www.stolaf.edu/people/hansonr> >>> http://www.stolaf.edu/people/hansonr >>> phone: 507-786-3107 >>> >>> >>> 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 >>> >>> >>> ------------------------------------------------------------------------------ >>> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA >>> Learn about the latest advances in developing for the >>> BlackBerry® mobile platform with sessions, labs & more. >>> See new tools and technologies. Register for BlackBerry® DevCon >>> today! >>> <http://p.sf.net/sfu/rim-devcon-copy1> >>> http://p.sf.net/sfu/rim-devcon-copy1 >>> _______________________________________________ >>> Jmol-users mailing list >>> <[email protected]>[email protected] >>> <https://lists.sourceforge.net/lists/listinfo/jmol-users> >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> ------------------------------------------------------------------------------ >> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA >> Learn about the latest advances in developing for the >> BlackBerry® mobile platform with sessions, labs & more. >> See new tools and technologies. Register for BlackBerry® DevCon today! >> <http://p.sf.net/sfu/rim-devcon-copy1> >> http://p.sf.net/sfu/rim-devcon-copy1 >> _______________________________________________ >> Jmol-users mailing list >> <[email protected]>[email protected] >> <https://lists.sourceforge.net/lists/listinfo/jmol-users> >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > <http://www.stolaf.edu/people/hansonr>http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > 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 > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > Learn about the latest advances in developing for the > BlackBerry® mobile platform with sessions, labs & more. > See new tools and technologies. Register for BlackBerry® DevCon today! > http://p.sf.net/sfu/rim-devcon-copy1 > > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > Learn about the latest advances in developing for the > BlackBerry® mobile platform with sessions, labs & more. > See new tools and technologies. Register for BlackBerry® DevCon today! > http://p.sf.net/sfu/rim-devcon-copy1 > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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
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