Hi
I usually add extra keywords in the "developers option" section of
the interface. I hope we will soon change the interface ti suite
current and the next version
of the program.
If unobserved reflections are present in the mtz file with missing
reflection flag then for map coefficients they are replaced by DFp.
It meant to b statistically more valid and
reflect the extected electron density. If they are not present then
nothing is done.
You can of course remove them from map calculations using sigma in
FFT calculation.
In the new version for all atoms f' and f'' are calculated. Although
only f' is used. If you give anom formfactor for a given atom then it
is used (at least it is the idea).
f' added to formfactors if the value is more than 0.01. Otherwise
they are not considered as anomolous scatterer.
In the older version these values were not calculated and used if you
gave them or used as if waverlength were CuKa edge.
I have to look and see why "Unknown atom for fpriem ad f2prime
calculation" is printed.
Regards
Garib
On 1 Jan 2008, at 16:16, Mark A Saper wrote:
Garib,
Many thanks for pointing out the differences. A couple of more
questions:
1. Could you tell me how 5.4.0033 by default handled the free and
missing reflections in map calculation. Also, is the ccp4i
interface suitable for the latest version of refmac --- I add the
extra keywords (like anom formfactor) in an "extra-param" file.
2. In version 5.4.0066 version I noticed this line in the log file:
Before the second run
Unknown atom for fprime and f2prime calculation
I didn't receive this error in the older version. Please explain.
I'm only specifying f' and f'' for the Selenium.
Thanks,
Mark
On Jan 1, 2008, at 10:29 AM, Garib Murshudov wrote:
Hi Mark
Could you please try again.
you are right. In case when you gave anom formfactor then f' was
added twice. In this version f' is added correctly. In the
previous version it was added in wrong place.
Geometry is tighter because we have fixed few bugs related with
chirality and vdw.
Garib
On 1 Jan 2008, at 14:40, Mark A Saper wrote:
Thanks for those pointing out my cut and paste error. Below are
the correct numbers. The first term of the formfactor is almost
twice as high compared to the other version. I suspect it is
because the newer version is using the wavelength in the
calculation, and the old version didn't.
Any help from the authors would be greatly appreciated.
Mark
Hi,
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
with .0066:
SE 17.0006 2.4098 5.8196 0.2726 3.9731 15.2372
4.3543 43.8163 -11.7969
The other major difference is that explicit weight that I was
using = 0.25 is weighting the geometry much more in .0066
compared with .0034. Also the refinement is not as well behaved
as it was in 0.0034.
What has really changed?
Mark
_________________________________
Mark A. Saper, Ph.D.
Associate Professor, Biophysics and Department of Biological
Chemistry
University of Michigan
3040 Chemistry Building
930 N University Ave
Ann Arbor MI 48109-1055
[EMAIL PROTECTED] phone (734) 764-3353 fax (734)
764-3323 Research summary
_________________________________
Mark A. Saper, Ph.D.
Associate Professor, Biophysics and Department of Biological Chemistry
University of Michigan
3040 Chemistry Building
930 N University Ave
Ann Arbor MI 48109-1055
[EMAIL PROTECTED] phone (734) 764-3353 fax (734)
764-3323 Research summary
