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
>>>
>>>-----------------------------------------------------------------
>>>
>>>
>>--------
>>
>>
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>>>
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>>
>
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--
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
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