There has been a serious problem in Refmac which apparently Garib
has fixed in this new release. When calculating structure factors
for models in space group P1 Refmac would "lose" some of the atoms.
I first ran into the problem by looking at the Electron Density
Server map for entry 3LEN. If you pull up that model and map in Coot
and go to the highest peak you will see a 44 sigma (ugh! substitute
"rms") peak centered on a sulfur atom that is clearly present in the
PDB. Looking in the neighborhood you will see that other atoms have
been lost as well. In fact you can line them up and see that all
atoms with Z between about -2.3 and -2.7 A are gone.
This was not some obscure problem, nearly every model with space
group P1 shows the same problem in the EDS maps. You can pull up
the map for 2XU1 and it shows the same problem - even the same Z
value band is affected.
Many of these P1 models are flagged in the EDS as having R values
that are not reproducible. I guess if you leave out enough atoms
you can cause the R value to degrade.
The EDS uses Refmac to calculate the structure factors and Fourier
coefficients. I've ran Refmac alone and reproduced this problem.
If you have refined a model with space group P1 in Refmac I suggest
you download the new version and see if your stats improve.
Dale Tronrud
On 5/27/2011 3:29 AM, Petr Kolenko wrote:
Dear colleagues,
Q2 is solved by new installation of Refmac. Many thanks for your time
and effort. I appreciate all your comments.
Petr
2011/5/27 David Cobessi<[email protected]>:
Dear Petr,
Before running Refmac, you have to remove the ANISOU line using pdbset for
example. In fact you should not add the TLS contribution to the output
coordinates when you use Refmac except in the last run before to deposit the
file into to PDB. Phenix removes it automatically.
Kind regards,
David
On 05/27/2011 10:57 AM, Petr Kolenko wrote:
Dear colleagues,
regarding Q2:
I do not use TLS parameters, the space group is P1, and yesterday I
tried to refine the structure with anisotropic ADP (60,000 reflections
against 50,000 parameters) - no positive maximums. Then I used the
anisotropic model as input and refined isotropically, the maximums are
there again.
I use refmac5.5.0100, is it really too late version? Seems to be
current version according the websites.
Many thanks.
Petr
2011/5/27 Jan Dohnalek<[email protected]>:
In the last months we have seen different versions of Refmac give
different
maps when displayed in Coot, i.e.
one version giving "nicer" agreement and no difference peaks in some
difficult areas and another version resulting in sharp differences where
it
was hard to build the protein. We did not investigate much further as
most
of the time use of two or three versions gave us a good picture of what's
going on ..probably a feature which would disappear with newer versions
anyway.
What's the version of Refmac you use, Petr?
Jan Dohnalek
On Thu, May 26, 2011 at 12:11 PM, Petr Kolenko<[email protected]>
wrote:
Dear colleagues,
I have two problems in two structure refinements using REFMAC5.
1) 1.8A resolution, zinc in the active site. Refinement using work
reflections - ADP for Zinc was about 14. Final refinement including
all reflections increase ADP to 20 or even higher values - followed by
very high positive difference density in position of the zinc. I have
tried also PHENIX, the same thing. I changed ADP manually to 14 and
only calculated maps (no refinement) look good. May I deposit the
structure using "manually" fixed ADP according to the best agreement
to the observed and difference electron density? By the way, it is
clear that this is zinc.
2) 1.9A resolution, about 600AA, all of them OK in electron density.
But, somehow, about ten atoms give very strong positive electron
density suggesting they are not taken into account in refinement. On
the other hand, ADPs are reasonable and seem to be refined. All of
these atoms are fully occupied. I tried to omit whole residues and
build them again, but the maxima appeared again. Using of PHENIX
resulted in no difference electron density for these atoms. I have
also tried to take PHENIX output to REFMAC, but the maxima are there
again. It is always one or two atoms from the same residues -
sometimes Calpha, sometimes Cbeta, sometimes C, sometimes NH1, but
still on the same five residues. Does anyone have any idea how to
solve this problem?
Many thanks for any response.
Petr
--
Petr Kolenko
[email protected]
http://kolda.webz.cz
--
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic
Tel: +420 296 809 390
Fax: +420 296 809 410
--
David Cobessi
Institut de Biologie Structurale
41, Rue Jules Horowitz
38027 Grenoble Cedex-1, France
Tel:33(0)438789613
33(0)608164340
Fax:33(0)438785122
