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 wrote:
> Got it! This had nothing to do with resolution, as it turns out. One
> simple line of code caused the problem. S
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 Han
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 fi
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
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
tmp = script("show isosurface");
isosurface ID "isosurface1" INLINE @tmp;
write "?.jmol";
Best
Alex
- Ursprüngliche Mail -
> Von: "Robert Hanson"
> An: jmol-users@lists.sourceforge.net
> Gesendet: Mittwoch, 18. Juli 2012 05:36:44
> Betreff:
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
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 lea
link to pngj https://www.dropbox.com/s/rcwwtns8rypi7qg/1crn.png
- Ursprüngliche Mail -
> Von: "Alexander Rose"
> 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 t
SAent from my Verizon Wireless Phone
- Reply message -
From: "Alexander Rose"
To: "jmol-users@lists.sourceforge.net"
Subject: [Jmol-users] artifacts inside protein surfaces
Date: Tue, Jul 17, 2012 7:38 am
Hi,
I think that was once solved but now there are arti
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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