Dear all,
On Thu, Jan 17, 2013 at 07:48:34AM -0800, Nat Echols wrote:
If I had to guess, I'd say that the output from Refmac is on an
approximately absolute scale, i.e. the volume-scaled density values
resemble the actual electron densities expected for the model. (I say
approximately
On 21/01/13 14:21, Clemens Vonrhein wrote:
Dear all,
On Thu, Jan 17, 2013 at 07:48:34AM -0800, Nat Echols wrote:
If I had to guess, I'd say that the output from Refmac is on an
approximately absolute scale, i.e. the volume-scaled density values
resemble the actual electron densities expected
On Mon, Jan 21, 2013 at 6:21 AM, Clemens Vonrhein
vonrh...@globalphasing.com wrote:
Just for the record: the map-coefficients written by BUSTER
(amplitudes 2FOFCWT and FOFCWT in the final 'refine.mtz' file) are on
the same scale as the model (amplitude FC) ie. on approximate absolute
scale.
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Hi Bernhard,
this sounds odd - wouldn't both maps be calculated from F/PHI by coot
itself? Why would Paul (Kevin?) make a difference there between phenix
and refmac5?
Curiously,
Tim
On 01/17/2013 10:23 AM, Bernhard Lohkamp wrote:
Hi Pedro,
this
Hi, Bernhard,
To clarify my previous e-mail, in both cases the maps are being
calculated from weighted coefficients from an MTZ file output by the program.
I tried calculating a weighted 2Fo-Fc map in CCP4i using the PHENIX
MTZ file and the end-result (red bars) was the same.
Pedro.
At
Density Fit Analysis with PHENIX map coefficients
Hi, Bernhard,
To clarify my previous e-mail, in both cases the maps are being
calculated from weighted coefficients from an MTZ file output by the program.
I tried calculating a weighted 2Fo-Fc map in CCP4i using the PHENIX
MTZ file and the end
(hesitating to restart an old flame war)
There has been a long-standing argument about scaling of electron density maps,
with many people deprecating sigma-scaling, for two reasons
1) in 2Fo-Fc type maps, sigma = RMS density is a function among other things
of the solvent content (smaller with
Excuse me if I'm wrong but should't the correlation coefficient
between Fo and Fc (which is what the Density Fit analysis is looking
at) be independent of this issue, provided Fo and Fc are on the same
scale ? And since the map is calculated from weighted 2Fo-Fc
amplitudes and phases the
Well, the problem seems to occur when Intensities are input to PHENIX
instead of structure factors. I repeated a run using Fobs, SigFobs as
input instead of IMEAN, SIGIMEAN and the Density Fit Analysis graph
looks normal.
At 16:57 17-01-2013, Nathaniel Echols wrote:
Actually, after some
