Oh! Duh..... silly me.... slinking back in search of the coffee
machine....
:)
On Tue, May 20, 2008 at 2:30 PM, Frieda Reichsman <[EMAIL PROTECTED]>
wrote:
> Hi Thomas,
> cavity3 is the object ID in this case, just a name Karl is giving the
> isosurface so as to be able to refer to it in later commands...
>
> isosurface [object id] [construction/mapping parameters] [surface
> object]...etc.
> *
> *
> Frieda
>
> //////////////////////////////////////
>
> Frieda Reichsman, PhD
> Molecules in Motion
> Interactive Molecular Structures
> http://www.moleculesinmotion.com
> 413-253-2405
>
> //////////////////////////////////////
>
>
>
>
> On May 20, 2008, at 4:34 PM, Thomas Stout wrote:
>
>
> Sorry to burst in on this thread, but I found it interesting and then the
> specification caught my eye:
>
> what does "cavity3" mean? I don't find that in the documentation for the
> isosurface command (
> http://chemapps.stolaf.edu/jmol/docs/?ver=11.6#isosurface). According to
> this, "cavity" should take two arguments, "cr" and "en", and so should look
> like: "cavity 1.2 10" (using the defaults). Is "cavity3" shorthand for
> "cavity 3.0 10" ?
>
> Thanks!
> -Tom
>
>
> On Tue, May 20, 2008 at 11:29 AM, Bob Hanson <[EMAIL PROTECTED]> wrote:
>
>> Oh, also, you might want to add OXY ot that list and also try
>> experimenting with the probe radius after the CAVITY parameter.
>> Something like:
>>
>> isosurface cavity3 minset 500 pocket ignore (hem,solvent,oxy) color
>> yellow cavity 1.0 translucent
>>
>> Karl Oberholser wrote:
>>
>> > Hi All,
>> > When I use these two commands, select protein; isosurface cavity3
>> > minset 500 pocket color yellow cavity translucent, with myoglobin
>> > (1mbo), I obtain two cavities. If I add ignore hem to give isosurface
>> > cavity3 minset 500 pocket ignore hem color yellow cavity translucent,
>> > I just obtain the cavity that is binding the heme. I would have
>> > expected to get the two other cavities along with the heme binding
>> > cavity. Am I missing something?
>> >
>> > Karl
>> >
>> >
>> >
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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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