Re: [Jmol-users] artifacts inside protein surfaces

[Robert H. <ha...@st...>]

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 <
ale...@we...> 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