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
, 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
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
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
users@lists.sourceforge.net
Subject: Re: [Jmol-users] Electron Density Map Demo
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 cont
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
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