I guess it was since summer and was only in cases if you gave
anom formfactor SE <number> <number>
If you did not then nothing was done.
Garib
On 3 Jan 2008, at 18:01, Ethan Merritt wrote:
On Thursday 03 January 2008 01:25, Boaz Shaanan wrote:
Is the wrong value pointed out by Ethan the reason why we tend
to nearly always see +ve difference peaks over Se-met after
refinement ?
Could be.
I have attached a plot of the net scattering factor for the two
sets of values.
I am curious as to exactly which version[s] of atomsf had the wrong
value for A1. The various old copies I have lying around on my disks
all contain the correct value.
Ethan
Just curious.
Regards,
Boaz
----- Original Message -----
From: Garib Murshudov <[EMAIL PROTECTED]>
Date: Wednesday, January 2, 2008 19:19
Subject: Re: [ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034
To: [email protected]
On 2 Jan 2008, at 17:15, Ethan Merritt wrote:
On Tuesday 01 January 2008 06:40, Mark A Saper wrote:
Well, I guess one shouldn't change versions of refmac in the
middle
of a structure refinement. What are the major
differences between .
0034 and .0066 ? I noted that form factors for the Se
atom have
changed dramatically even though I'm using the same " anom
formfactor>> SE -8.13 5.05 " command. Is this because the
program is now using
the wavelength on the .MTZ file ?
with .0034:
SE 8.8706
2.4098 5.8196 0.2726
3.9731 15.2372
4.3543 43.8163 2.8409
The first coefficient here is wrong.
with .0066:
SE 17.0006
2.4098 5.8196 0.2726
3.9731 15.2372
4.3543 43.8163 -11.7969
These are the values given for a1, b1, ... a4, b4 in Table 6.1.1.4
of International Tables for Crystallography Volume C (1995).
The value of c (-11.7969) corresponds to an f' value of
-14.6378 (= -11.7969 - 2.8409)
This could only be possible at the inflection point of the Se
anomalous scattering curve, and only for a beam with a very narrow
bandwidth. Current generation beamlines more
typically yield an
effective f' of -5e to -10e in practice.
We have corrected it. It was due to double addition of f' (one
from
anom formfactor and one from a la crossec calculation). Now it
should
not happen
Garib
--
Ethan A
Merritt Courier Deliveries: 1959 NE Pacific
Dept of Biochemistry
Health Sciences Building
University of Washington - Seattle WA 98195-7742
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan‎
--
Ethan A Merritt Courier Deliveries: 1959 NE Pacific
Dept of Biochemistry
Health Sciences Building
University of Washington - Seattle WA
98195-7742<Se_scatter.gnu><Se_scatter.pdf>
