Hi,
the tip with set 1 is great.
it's much cleaner now, though I found some fragments, i.e.
load =1u19;
isosurface molecular;
isosurface set 2;
I also have some file with multiple models where I now get only the fragments
but not the actual surface. (can't sent you that file but if needed I can try
to reproduce it with other files);
This somehow kills Jmol (I still get messages in the console when I click
somewhere on atoms but the display is unresponsive and no isosurface is shown):
load =1u19;
load append =1u19;
# frame all; # this solves it
isosurface select {1.1} molecular;
loading of the .jmol from this does not work, some syntax error:
# trying to get the isosurface into the state to trade a slightly bigger file
size for faster loading
load =1crn;
isosurface ID "isosurface1" select {*} molecular;
isosurface ID "isosurface1"
tmp = script("show isosurface");
isosurface ID "isosurface1" INLINE @tmp;
write "?.jmol";
Best
Alex
----- Ursprüngliche Mail -----
> Von: "Robert Hanson" <hans...@stolaf.edu>
> An: jmol-users@lists.sourceforge.net
> Gesendet: Mittwoch, 18. Juli 2012 05:36:44
> Betreff: Re: [Jmol-users] artifacts inside protein surfaces
> OK, that should be fixed. See
> http://chemapps.stolaf.edu/jmol/Jmol-13.zip
>
> I'm not 100% sure my solution is ideal, but it should be much cleaner.
> This only affects isosurface SOLVENT/MOLECULAR surfaces that do not
> include CAVITY in their parameters.
>
>
> On Tue, Jul 17, 2012 at 6:08 PM, Robert Hanson < hans...@stolaf.edu >
> wrote:
>
>
> Yes, there are improper internal VDW surfaces being displayed. Hmm...
>
> The short-term solution is to use "SET 1" in that isosurface command:
>
> isosurface solvent set 1
>
> but it's definitely a bug. I will look into it. I can find
>
> Thanks. Checking in my archives, the problem was there in 11.1 at
> least (back when I got started in Jmol.) This certainly will be a
> challenge. Why do I feel like I've fixed this before?
>
> Bob
>
>
>
>
>
> On Tue, Jul 17, 2012 at 7:30 AM, Alexander Rose <
> alexander.r...@weirdbyte.de > wrote:
>
>
> link to pngj https://www.dropbox.com/s/rcwwtns8rypi7qg/1crn.png
>
> ----- Ursprüngliche Mail -----
> > Von: "Alexander Rose" < alexander.r...@weirdbyte.de >
> > An: jmol-users@lists.sourceforge.net
> > Gesendet: Dienstag, 17. Juli 2012 13:36:26
> > Betreff: artifacts inside protein surfaces
>
>
> > Hi,
> >
> > I think that was once solved but now there are artifacts inside
> > protein surfaces. See attached pngj, created on
> > http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm -
> > Version
> > 12.3.32_dev, I've seen it also in 12.3.33.
> >
> >
> > Best 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
>
>
>
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