hmm. yes, something there....
On Sun, Aug 29, 2010 at 6:37 PM, Frieda Reichsman <frieda...@mac.com> wrote:
> Comments below.
>
> On Aug 29, 2010, at 1:05 PM, Robert Hanson wrote:
>
> On the other hand, the WITHIN option still works with any surface, so if
> you use that, the isosurface from a JVXL file might be truncated. I don't
> think isosurface SLAB or CAP has any action in this regard -- though maybe
> it should....
>
>
> nope, did not use "select within(whatever)"
>
>
> On Sun, Aug 29, 2010 at 11:59 AM, Robert Hanson <hans...@stolaf.edu>wrote:
>
>> I can't imagine that anything having to do with the creation of the
>> isosurface from a JVXL file has anything to do with atom selection.
>
>
> Well, that's a relief! ...it's always nice to know that one's ground-level
> assumption is generally accepted. :)
>
>
> But, yes, mapping would probably be that way. Right.... For instance?....
>>
>>
> For instance, using this isosurface command:
> isosurface surf1 "3d/finalsurface.jvxl" map property_x color translucent -1
> colorscheme "user";
>
> if I say "select protein" before it, the surface is truncated in several
> places
>
> if I say "select :b" the surface is fully intact. Let me know if you want
> the files...
>
> Frida
>
>
>
>
>>
>> On Sun, Aug 29, 2010 at 12:46 AM, Frieda Reichsman <frieda...@mac.com>wrote:
>>
>>> Hi,
>>>
>>> Does the display of an isosurface (the area it covers) vary depending on
>>> what is selected at the time you call the jvxl file? I don't recall this,
>>> but it is true in 12.0.8 and 12.0.10. I expect the surface in a jvxl file to
>>> be the same surface all the time... but perhaps somehow I have been lucky
>>> enough not to trip over this before.
>>>
>>> Or perhaps it varies when you are mapping something to the surface, e.g.,
>>> isosurface surf1 "3d/finalsurface.jvxl" map property_x color translucent
>>> -1 colorscheme "user";
>>> but then I would expect the color might vary with the selection, but not
>>> the surface itself.
>>>
>>> Frieda
>>>
>>>
>>>
>>> On Aug 27, 2010, at 3:47 PM, Robert Hanson wrote:
>>>
>>> Jmol users --
>>>
>>> The isosurface/JVXL problems in 12.0 and 12.1 have been fixed. (Jmol 12
>>> could crash opening older nonXML JVXL files.)
>>>
>>> http:/chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
>>>
>>> 12.0.10 will have that in it, probably next week.
>>>
>>> -- Bob
>>>
>>> On Mon, Aug 23, 2010 at 8:41 AM, Pshemak Maslak <p...@chem.psu.edu> wrote:
>>>
>>>> Hello,
>>>>
>>>>
>>>> 4. 12.08 has difficulty in displaying jvxl file written by 11.8. It does
>>>> it very slowly (several minutes) and --after finally loading -- the
>>>> model cannot be interacted with. I have encountered only one example of
>>>> this difficulty, and the jvxl file re-written with 12.08 Jmol works
>>>> fine. Could this have anything to do with the changes in the spartan
>>>> file reader? (my jvxl files are based on smol spartan files)
>>>>
>>>>
>>>> PM
>>>>
>>>>
>>>>
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>>>
>>>
>>>
>>> --
>>> 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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>>
>>
>> --
>> 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
>>
>
>
>
> --
> 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
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue and
> speed time-to-market. Join now, and jumpstart your future.
>
> http://p.sf.net/sfu/intel-atom-d2d_______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
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>
--
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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Be part of this innovative community and reach millions of netbook users
worldwide. Take advantage of special opportunities to increase revenue and
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