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.
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 :
> Dear Petr,
> Before running Refmac, you have to remove the ANISOU line using pdbset for
> example. In fact you should not add the T
Dear Petr
Newer version of refmac is 5.6 and it should be available from ccp4 soon.
Meanwhile you can try this version from this website
http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.6_linux.tar.gz
There are versions for mac etc also.
regards and I hope you will sort it
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 ma
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 in
Hi Petr,
a few things to consider:
1) Fourier truncation ripples:
- CCP4 Newsletter
http://www.ccp4.ac.uk/newsletters/newsletter42/content.html
On the Fourier series truncation peaks at subatomic resolution
Anne Bochow, Alexandre Urzhumtsev
- Pages 52-55 here:
htt
If you are using TLS refinement the please check TLS definitions.It may be that
atoms for which you have positive density are not in TLS definitions.
Try to use without TLS.
regards
Garib
On 26 May 2011, at 11:11, Petr Kolenko wrote:
> Dear colleagues,
>
> I have two problems in two structure
regarding the first question - is it now not much more common to refine only
against work reflections, and not do a final refinement agains all reflections?
(avoids the problem rather than solve it, I admit)
regarding the second question - if you take the model from refmac and calculate
a map us
Dear colleagues,
Thanks for the responses. But, Zn occupancy is not an issue. There is
positive maximum, not negative. And Q2, I tried to do it in coot and
also in text editor. Both results were the same. And I double-checked
the line for the atoms in the pdb file for ADP and occupancy.
Regarding
60% occupied Zn site perhaps ?
Q2 do you have leftover atoms from a previous dual conformation refinement ?
Try deleting the corresponding residues in a texteditor and not coot to ensure
they are really gone, then rebuild the section into the new diff- map.
Jürgen
..
Jürgen
How very odd!
I have no ideas on the Zn phenonema - what do the R factor plots look
like against resolution - is there some aberrant reflection which was
part of the FreeR set? The theory is that excluding 5% of the data
should not affect the model seriously at all..
Re the 2nd point. Two
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
If you have used TLS the B factors listed for the residues are the
residual values AFTER the TLS is applied so they are correctly
restrained to be quite close - the differences in the molecules should
be expressed in the hard-to-visualise TLS parameters.
The first check is to run
TLSANL and as
Hello - I have nearly completed a crystal structure at 2.6 A resolution. There
are 3 monomers per asymmetric unit (same protein in different conformations),
and I have been using non-crystallographic symmetry during the refinement
process (REFMAC5). I have been isotropically refining B-values
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