-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Pavel,
surely technically you are right. Practically I would like to see the
face when you next hand over a set of structure factors to a
pharmaceutist or biologist with the words "please go ahead, design
your drug" ;-)
Best,
Tim
On 05/21/2014 04
On 21/05/14 14:57, Remie Fawaz-Touma wrote:
Thank you so much for your replies.
CCP4 refinement file is showing warnings that the Glc units are at
distance (1.4-2.1A) greater than the acceptable one by the program
(1.33A) from each other even though I got the model from a published
pdb file.
the R-factor is a complicated thing that depends on things like
> weighting factors and solvent model - several things that are not part
> of your model and that need to be adjusted by the refinement program
> during refinement.
>
I think a more accurate is "are not part of your ATOMIC model".
Bul
Thank you so much for your replies.
CCP4 refinement file is showing warnings that the Glc units are at distance
(1.4-2.1A) greater than the acceptable one by the program (1.33A) from each
other even though I got the model from a published pdb file. so the pdb file
generated only shows me dott
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Remie,
the R-factor is a complicated thing that depends on things like
weighting factors and solvent model - several things that are not part
of your model and that need to be adjusted by the refinement program
during refinement.
That's why I th
Hi all,
I am trying to refine a structure in CCP4 and the final R factor is about 1%
lower than the initial but for the first “task/cycle” within the same
refinement job in CCP4, R factor starts off higher than the input data R factor.
I have a structure with multiple sugars attached, I did the
I am afraid there is no real solution except to read the paper!
And even that doesnt help if you suspect the merging..
There is lots of discussion about the merit of depositing UNMERGED
data - and that would certainly help developers. Add your voice to the
request!
Eleanor
On 30 January 2014 08:2
I think the name says it all:
"Rmerge"
"merged data"
So no, there wouldn't be. You'll find it in the header.
On 30/01/2014 08:18, Fulvio Saccoccia wrote:
Dear ccp4 users,
does anyone know if there is a way to (re)calculate the Rmerge from a
deposited .cif file in PDB?
In this case is
Dear ccp4 users,
does anyone know if there is a way to (re)calculate the Rmerge from a
deposited .cif file in PDB?
In this case is an already merged structure factor file.
I know that the EDS from Uppsala makes it, providing the PDB entry, but I
need a procedure in order to do it by myself.
I see
Dear Daniel,
A very good question. I have seen R_d plots jumping up and down, most often in
low-symmetry space groups. I think the "mountains" are due to residual
systematic differences between symmetry-related observations, differences that
the scaling could not compensate for whatever reason.
Dear all,
I am using xds (with graphical interface xdsgui) to process several
diffraction data of a membrane protein that I have crystallized. At the
end, I run XDSSTAT in order to check the statistic parameters of the
process and my attention is captured by the R_d plot: R_d drops during
the
that doesnt seem too bad an Rfactor to me! What do you expect?
Eleanor
On 27 August 2013 09:59, Afshan Begum wrote:
> Hi ccp4 experts,
>
> I have collected diffraction images to 0.96 Angstrom resolution to the edge
> of the detector. One data set give me the full completeness and
> below i have
Hi ccp4 experts,
I
have collected diffraction images to 0.96 Angstrom resolution to the edge
of the detector. One data set give me the full completeness and
below i have pasted my statistic values got from XDS.
I have cut off data at 1.12 A which seems to be quite nice regarding all
neces
As always, look at the crystal packing of the MR
solutions. That is a quick way to reject incorrect space group
solutions. I never realized Phaser had the issue you described with the
SGALTERNATIVE setting, but to be honest, I've always run it in "manual"
mode, i.e., I set up separate jobs in a
How certain are you of the space group?
I ask because in all versions of PHASER that I have used to date, it chooses
the space group (when SGALTERNATIVE is set) after placing the first molecule
and with additional molecules it then assumes the space group result from the
first molecule is the c
On Sun, Oct 3, 2010 at 6:34 PM, J. Preben Morth wrote:
> hi
> remember to reindex your data to P21212 in case you used Phaser to search
> all alternative orthorhombic SG's and it found P22121
> Preben
>
>
Hi, re-indexing the data without also remembering to transform the
co-ordinates (using the m
the reindexing have no effect on the R-factor, I did indeed mean to remember to
transform the co-ordiantes according to the indexing :-)
On 04/10/2010, at 11.27, Ian Tickle wrote:
>
> On Sun, Oct 3, 2010 at 6:34 PM, J. Preben Morth wrote:
> hi
> remember to reindex your data to P21212 in case y
Is that necessary?
Eleanor
J. Preben Morth wrote:
hi
remember to reindex your data to P21212 in case you used Phaser to search all
alternative orthorhombic SG's and it found P22121
Preben
On 03/10/2010, at 04.56, Jack Russel wrote:
Hi all,
I have collected a data at 2.9 Å and the solved
hi
remember to reindex your data to P21212 in case you used Phaser to search all
alternative orthorhombic SG's and it found P22121
Preben
On 03/10/2010, at 04.56, Jack Russel wrote:
> Hi all,
>
> I have collected a data at 2.9 Å and the solved the structure using phaser .
> the space group c
1) Rigid body refinement wont reduce R factors much more than this -
start restrained refinement with NC restraints..
2) And yes - at low resolution you could expect a large difference
between R and rfree
3) With such high NC symmetry is there any possibility of another SG?
Eleanor
Jack Rus
A handy way to do what Paul suggests is the Zanuda server at York
which will try refinement in all lower symmetries ...
From the first email though two things are unclear:
1. How good was the Phaser solution (eg z-score?) ?
2. Did you only try rigid body fitting as you wrote? (I find regid
b
Try a lower symmetry, e.g. P21 or P1 with one or two octamers in the asymmetric
unit (well, unit cell for P1), but you already know your packing so no problem
solving it.
It can sometimes be very subtle and your model refinement will be the most
sensitive test for the correct space group - so do
Hi all,
I have collected a data at 2.9 Å and the solved the structure using phaser .
the space group comes to be P2 21 21. There are 4 molecules in Assymetric unit
and an octamer is generated according to the symmetry. But after repeated
rounds of rigid body refinement with REFMAC5 and model b
On 10 Sep 2009, at 19:29, Pavel Afonine wrote:
Hi Sylvia,
although modern MR programs perform rigid body refinement, it may be
worth of giving a try a novel rigid body refinement protocol
implemented in phenix.refine (MZ rigid-body refinement protocol),
that has very high convergence rad
Hi Sylvia,
although modern MR programs perform rigid body refinement, it may be
worth of giving a try a novel rigid body refinement protocol
implemented in phenix.refine (MZ rigid-body refinement protocol), that
has very high convergence radius:
J. Appl. Cryst. (2009). 42, 607-615. "Automatic
On 09/10/2009 12:17 PM, Sean Seaver wrote:
Hello Sylvia,
Two issues I would consider:
1) recheck the space group
2) make sure that I had selected a good model for my MR search
All the Best,
Sean
Hi Sylvia,
If you have just used rigid body refinement - the Rfactor might be high
until y
It would not necessarily be unusual for an initial
MR solution to have an R-factor of 45-48%, depending on the MR program
used and quality of the search model. However, after an initial
restrained refinement in Refmac, a good solution should drop pretty
smartly from there. Some issues to consid
Hello Sylvia,
Two issues I would consider:
1) recheck the space group
2) make sure that I had selected a good model for my MR search
All the Best,
Sean
Hi everyone
I am new to solving crystal structures so apologies for the simple
question
I am solving a structure using molecular replacement. I have refined my
structure with refmac however the R-factor and R-free do not seem to go
down with successive rounds of refinement. The initial
29 matches
Mail list logo
