On Sat, Jul 21, 2012 at 12:37 PM, Alexander Rose <
alexander.r...@weirdbyte.de> wrote:
> Hi,
>
> the tip with set 1 is great.
>
>
well, it's really a hack until you get the latest version.
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.
I did notice there some imperfections in the surface -- gaps -- that are
the result of the default resolution being too low. you could try adding
RESOLUTION 1.0 in there to make that better.
> 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);
>
>
Make sure you try that with the latest,
http://chemapps.stolaf.edu/jmol/Jmol-13.zip (uploading now)
I just fixed an error there in my calculation of the volume of a sphere.
This removes a lot of the fragments.
I'm still going to think about this, but the main issue is that you have a
case where the default resolution is too low. Once the resolution (points
per Angstrom) gets to about the size of the solvent radius in Angstroms,
then there is going to be trouble. A solvent molecule can fit between the
grid points. OK, I have set a minimum default resolution, and this may slow
down your calculation someone or use too much memory.
States saved that use isosurface SET n may need to be generated again, as
the number of sets is different now.
see http://chemapps.stolaf.edu/jmol/Jmol-13.zip
By the way, you might want to use isosurface SOLVENT instead of MOLECULAR.
Do you really want the surface around the water molecules?
Bob
# 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.
--Bob
--
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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