In Jmol 11.9.20_dev, the transfer of a terminal alkene or a primary
amine from both Marvin Sketch and JME followed by minimize
addHydrogens results in coincident hydrogen atoms. Both hydrogen atoms
are in the molfile, they are just coincident. There may be other cases
of coincident hydrogen atoms,
Thanks, that really helps. Unfortunately, that won't work. I don't know if
it's just different fields using the same data files, but the files I have
that are from electron diffraction simply display nothing when you use that
cutoff. Still, it might be useful to implement something like a sigma opt
Robert Hanson wrote:
> Keep talking, Rich. I don't quite have it.
>
> I have a file of numbers. An isosurface is produced not by contouring
> but by finding the surface that intersects that cube of numbers at a
> specific "cutoff" value.
>
> > dmin dmax dmean (density min max mean)
> >
>
Keep talking, Rich. I don't quite have it.
I have a file of numbers. An isosurface is produced not by contouring but by
finding the surface that intersects that cube of numbers at a specific
"cutoff" value.
> dmin dmax dmean (density min max mean)
> >
> > rms
>
>1 sigma = 1 esd = 1 rmsd*rmsd
>
> write "3hyd.jvxl"
>
> (from the application or signed applet)
Or pop-up menu > File > Save JVXL Isosurface
with a nice Save As dialog that lets you see/choose where it is going
:-)
--
Throughout its 18-year histor
Eric, ah, so this IS something you haven't started using. No better time
than now. You will really like this. The command, after displaying the
isosurface, is
write "3hyd.jvxl"
(from the application or signed applet)
then
isosurface color yellow "3hyd.jvxl" mesh nofill
will call it up. It will
On Tue, 19 Jan 2010 14:03:32 -0600, Robert Hanson
wrote:
> Is that in the file somewhere? What I have is
>
> dmin dmax dmean (density min max mean)
>
> rms
>
> Now, I DON'T think the "rms" is really "rms" -- I think it's rms
deviation,
> but I could be wrong about that. What seems to work as a
--- On Tue, 1/19/10, Robert Hanson wrote:
From: Robert Hanson
Subject: Re: [Jmol-users] Electron Density Map Demo
To: jmol-users@lists.sourceforge.net
Date: Tuesday, January 19, 2010, 2:08 PM
Great to hear that, Eric. I would be very interested in seeing on that last
page a comparison of loadi
Is that in the file somewhere? What I have is
dmin dmax dmean (density min max mean)
rms
Now, I DON'T think the "rms" is really "rms" -- I think it's rms deviation,
but I could be wrong about that. What seems to work as a reasonable default
is
dmean + 2*rms
But that could be a complete misuse
Talk about timing, I'm sitting at my desk reading a paper where they used
the term and was JUST about to go look it up. You all are incredible!
- brian
-Original Message-
From: r...@ellerbach.com [mailto:r...@ellerbach.com]
Sent: Tuesday, January 19, 2010 2:27 PM
To: jmol-users@lists.sou
The "sigma" is the esd (estimated standard deviation) for the value of the
electron density at any grid point. So if the electron density calculations
provide an esd of 1.2 electrons per cubic angstrom the 1 sigma contour
lines would be at 1.2, the 2 sigma lines at 2.4, 3 sigma at 3.6 etc.
Rich
O
Great to hear that, Eric. I would be very interested in seeing on that last
page a comparison of loading the ccp4 file and a JVXL version of it.
Main question is: "What's a sigma?"
On Tue, Jan 19, 2010 at 12:54 PM, Eric Martz wrote:
> I have put an all new demo for electron density maps at
> h
I have put an all new demo for electron density maps
athttp://www.umass.edu/molvis/tests/jmol_edmEverything works!! (as far as I can
tell ... now I need to learn more from the crystallographers here before I can
take it further).
As for the default sigma value for the contours, I have talked to
Here's another new option "set zshadepower" that could be fun to experiment
with. Notice the intense fog
http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm?load%20quartz-action.png;set%20slabcleanly;set%20zshadepower%203
On Tue, Jan 19, 2010 at 6:45 AM, Robert Hanson wrote:
> A wee bi
A wee bit better perhaps, with this option I'm experimenting with:
http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm?load%20quartz-action.png;set%20slabcleanly
On Tue, Jan 19, 2010 at 6:42 AM, Robert Hanson wrote:
> Mouse wheel -- right, Rolf. That is a change. That was toned down bec
Mouse wheel -- right, Rolf. That is a change. That was toned down because it
was just way too difficult to control (in my opinion), but we can revert
that if you think what we have now is just too slow. Let's talk about that.
Since I don't have a mouse wheel, I'm probably not the one to ask, but th
On 01/18/2010 09:03 PM, Eric Martz wrote:
> I have made a little demonstration of visualization electron density maps in
> Jmol, showing off some of Bob's recent innovations.
> http://www.umass.edu/molvis/tests/jmol_edm_test4/
>
> This new capability of Jmol is just fantastic!
>
I agree!
While
17 matches
Mail list logo
