Is the R factor for the best solution really > 40% - if so there must be
some major errors to correct.
Eleanor
On Fri, 31 Jul 2020 at 11:08, John R Helliwell
wrote:
> Dear Rafal,
> The difference map you show in your attachment has an echo of the main
> structure sort of look. So, I suggest you
Dear Rafal,
The difference map you show in your attachment has an echo of the main
structure sort of look. So, I suggest you examine your diffraction images
specifically looking out for a supercell of weak intensity spots, not picked up
by the autoindexing, between the main lattice of
Dear Rafal,
with such a small molecule, and if you really have 1.0A resolution, you
should be able to solve the structure by direct methods with shelxt. By
default, shelxt searches all space groups in the Laue group. The output
will not be very practical to assign residue, etc. but at least it
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board Im Auftrag von Rafal Dolot
Gesendet: Donnerstag, 30. Juli 2020 14:06
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Problems with refinement of nucleic acid
structure
EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
Dear all,
Thank you for the response. I will try to explain it more precisely.
The molecule of interest is a duplex with 9 nt length, but is paired on
the length of eight bases, with overhangs at ends. Molecules form a
parallel strings across the crystal lattice, parallel to C-axis, because
>> conformation, so it might be a good idea to test if this is also true for
>> nucleotides.
>>
>> Best, Herman
>>
>> -Ursprüngliche Nachricht-
>> Von: CCP4 bulletin board Im Auftrag von Rafal Dolot
>> Gesendet: Mittwoch, 29. Juli 202
gliche Nachricht-
> Von: CCP4 bulletin board Im Auftrag von Rafal
> Dolot
> Gesendet: Mittwoch, 29. Juli 2020 14:42
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] [ccp4bb] Problems with refinement of nucleic acid
> structure
>
> EXTERNAL : Real sender is owner-ccp..
, 29. Juli 2020 14:42
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Problems with refinement of nucleic acid structure
EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
Dear CCP4 users,
I'm working on the another nucleic acid duplex structure. After several stages
of rebuilding
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
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
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
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 david.cobe...@ibs.fr:
Dear Petr,
Before running Refmac, you have to remove the ANISOU line using pdbset for
example. In fact you
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.
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
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
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
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
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
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
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