ps -- [Note that internal cavities will show up with isosurface SOLVENT or
isosurface MOLECULAR as sets with negative volume.]
On Mon, Jul 23, 2012 at 1:41 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> Got it! This had nothing to do with resolution, as it turns out. One
> simple line of code caused the problem. See
> http://chemapps.stolaf.edu/jmol/Jmol-13.zip
>
> Thank you so much, Alexander, for pointing this out. It's actually been
> there a very long time.
>
> On Mon, Jul 23, 2012 at 12:12 PM, Robert Hanson <hans...@stolaf.edu>wrote:
>
>> Yes, I see that, Alexander. Thanks for the PNGJ file - that is really a
>> great way to send issues to me. I wish everyone would do that.
>>
>> I'll study this some. I really think it is an artifact of the poor
>> resolution. Molecular surfaces are notoriously challenging to produce, and
>> this one does just fine in a localized sense. But at that resolution --
>> even 2.0 -- you are seeing artifacts.
>>
>> I'm definitely interested in fixing this.
>>
>>
>>
>> On Sun, Jul 22, 2012 at 10:13 AM, Alexander Rose <
>> alexander.r...@weirdbyte.de> wrote:
>>
>>> Hi Bob
>>>
>>> using # Jmol state version 13.0.RC2 2012-07-21 19:52;
>>>
>>> > load =1u19;
>>> >
>>> > OK, here you have three isosurfaces. set 1 is the outer set, but there
>>> > are two cavities, each of which is big enough to hold a molecule of
>>> > water.
>>>
>>> there is something strange going on, I still get those fragments
>>>
>>> load =1u19;
>>> isosurface resolution 2.0 solvent;
>>> isosurface set 2;
>>>
>>> pngj: https://www.dropbox.com/s/o6q7dudwj48k4ht/1u19.png
>>>
>>> > By the way, you might want to use isosurface SOLVENT instead of
>>> > MOLECULAR. Do you really want the surface around the water molecules?
>>>
>>> these were just minimal examples nothing I actually used, thanks though
>>>
>>> > # trying to get the isosurface into the state to trade a slightly
>>> > bigger file size for faster loading
>>> >
>>> >
>>> > use
>>> >
>>> > write xxx.jvxl
>>> >
>>> > then immediately replace the isosurface with that using
>>> >
>>> > isosurface delete
>>> > isosurface "xxx.jvxl"
>>> >
>>> > then write the file as a PNGJ or JMOL. This should be very compact and
>>> > very fast to load.
>>>
>>> yes that's ok but I did not mention that I want to use this in the
>>> applet and make it as automatic as possible, without the detour to the file
>>> system, which requires user interaction.
>>>
>>> The problem seems to be in
>>> jmol.shapesurface.Isosurface.java::getMeshCommand()
>>>
>>> cmd = TextFormat.simpleReplace(cmd, ";#", "; #");
>>> int pt = cmd.indexOf("; #");
>>> if (pt >= 0)
>>> cmd = cmd.substring(0, pt);
>>>
>>> We could look for " inline " in cmd? Ahh, thats not enough, as you can
>>> do "isosurface ID inline inline @tmp". A regex perhaps:
>>>
>>> if( cmd.toLowerCase().indexOf("inline") >= 0 &&
>>> !cmd.matches("(?i)id\s*['\"]?\s*inline\s*['\"]?") ){ // not tested
>>> cmd = TextFormat.simpleReplace(cmd, ";#", "; #");
>>> int pt = cmd.indexOf("; #");
>>> if (pt >= 0)
>>> cmd = cmd.substring(0, pt);
>>> }
>>>
>>> Well, not perfect, then we would not strip comments from the inline
>>> command. How did one get these comments anyway?
>>>
>>>
>>> Alex
>>>
>>>
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>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> 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
>>
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> 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
>
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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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