If you have unmerged data try running it through
pointless/aimless/ctruncate.
That analyses twin fractions very carefully and with that twin law you
should see some evidence of 6 fold symmetry but less pronounced than for
the 3 and 2 fold symmetry operators..
Eleanor
On 11 June 2015 at 01:03, Men
Thank you Jacob and Ethan!
I haven't put water molecules into the density blob, which aren't many out
there, but I fitted the ligands in already. Molbrobity statistics are not
yet great, since there are 13.5% rotamer outliers.
Will adjust the models manually, and try refmac and TLS refinement.
T
On Wednesday, 10 June, 2015 17:35:25 Mengbin Chen wrote:
> Hello everyone,
>
> I am refining a 2.5 angstrom structure whose phase is solved by molecular
> replacement with a search probe determined by SAD with 3 angstrom
> resolution. While I am able to see densities of a bunch of water molecules
@JISCMAIL.AC.UK
Subject: [ccp4bb] twinned data refinement
Hello everyone,
I am refining a 2.5 angstrom structure whose phase is solved by molecular
replacement with a search probe determined by SAD with 3 angstrom resolution.
While I am able to see densities of a bunch of water molecules and ligands in
Hello everyone,
I am refining a 2.5 angstrom structure whose phase is solved by molecular
replacement with a search probe determined by SAD with 3 angstrom
resolution. While I am able to see densities of a bunch of water molecules
and ligands in the MR solved structure, which means that the phase
Dear all
Lately i have found my crystals to be pseudomerohedrally twinned with a
twin fraction of 0.22..but on doing twin refinement nothing much is
changing in terms of statistics as compared to the previously solved data
which did not include twin refinement (in present case the data is solved
a
Or put all files into pointless..
It will read XDS and do the indexing checks
Eleanor
On 19 Oct 2012, at 12:45, vellieux wrote:
> Well, the first thing I note is that P6(3) is a polar space group.
>
> Hence what I would do myself is the following:
>
> take your crystal 'number 1' (as a referen
Dear Iris,
just to add to Fred's posting: since XDS Version June 2, 2008 re-indexing is no
longer necessary if REFERENCE_DATA_SET is used - XDS then does the re-indexing
automatically in the CORRECT step. This makes it very easy to avoid the problem
of alternative indexing in space groups like
Well, the first thing I note is that P6(3) is a polar space group.
Hence what I would do myself is the following:
take your crystal 'number 1' (as a reference);
take the results of XDS for crystal number 2 (XDS_ASCII.HKL) and reindex it;
try to see which of the original XDS_ASCII or the reinde
Hello everybody,
I collected datasets with a resolution to 2.8A from 3 crystal grown in the
same condition. The space group seems to be P63. Statistic of XSCALE.LP
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS
Hello,
I am afraid that you aren't saying (writing) enough to describe the
problem(s) you are facing...
Twin fraction ? How many crystals were used to collect the diffraction
data (remember that there are polar space groups, where c going "up" is
different from c going "down") etc etc. Witho
Hello everybody,
I collected data to 2.8A with the space group P63 but they seems to be twinned.
I tried phenix refinement with the twin law I got from Xtriage but the model
looks quiet weird...
Hope that somebody can help me with this problem.
Kind regards,
Iris
_
- Original Message -
From: "Clayton, Gina Martyn"
Date: Friday, October 1, 2010 21:28
Subject: [ccp4bb] Twinned data
To: CCP4BB@JISCMAIL.AC.UK
> Hi there
>
> Just wondering if anyone has any suggestions how I can deal, if
> possible, with the following situation -
Sent: Friday, October 01, 2010 6:35 PM
To: Clayton, Gina Martyn
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Twinned data
If you really have the systematic absences for P41 or P43 then you must
have (at least) four molecules in the cell, twinning cannot reduce this.
Since a solvent content of 1
If you really have the systematic absences for P41 or P43 then you must
have (at least) four molecules in the cell, twinning cannot reduce this.
Since a solvent content of 16% is too low, the most likely explanation
is that it is not twinned but that the protein is smaller than the one
you are ex
Hi there
Just wondering if anyone has any suggestions how I can deal, if
possible, with the following situation -. My first encounter with
twinned data...
which initially indexed as p43/p41 cell dimensions 58.4 58.4 61 90 90
90.
Having seen the Matthews Coefficient for the solvent content of th
ilto:ccp...@jiscmail.ac.uk] Im Auftrag von
> Walter Kim
> Gesendet: Monday, March 16, 2009 7:22 AM
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [ccp4bb] Twinned data and maps
>
> Hi again,
>
> Thanks for your insight into refinement tools for twinned data. I have a
> coup
Dodson
Gesendet: Monday, March 16, 2009 12:52 PM
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps
But dont all twinned refinement programs output detwinned terms for a map?
Certainly REFMAC and SHELX do.
Eleanor
Clemens Steegborn wrote:
> Hi Walter,
>
> You
o try
Phenix ...
Best
Clemens
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag
von
Walter Kim
Gesendet: Monday, March 16, 2009 7:22 AM
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Twinned data and maps
Hi again,
Thanks for your insight into refin
LWAYS to try more than one program, and also to try
Phenix ...
Best
Clemens
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von
Walter Kim
Gesendet: Monday, March 16, 2009 7:22 AM
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Twinned data and
program, and also
to try
Phenix ...
Best
Clemens
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von
Walter Kim
Gesendet: Monday, March 16, 2009 7:22 AM
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Twinned data and maps
Hi again,
Than
o:ccp...@jiscmail.ac.uk] Im Auftrag von
Walter Kim
Gesendet: Monday, March 16, 2009 7:22 AM
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Twinned data and maps
Hi again,
Thanks for your insight into refinement tools for twinned data. I have a
couple of twinned data sets that are nearly perf
I am not sure if there is any way of avoiding model bias if the
coordinates are included regardless of whether there is twinning or not
- my preferred method is to set the occupancies of suspect regions to
0.00 then do refinement of the better parts of the model and then check
maps again and re
Hi again,
Thanks for your insight into refinement tools for twinned data. I have a
couple of twinned data sets that are nearly perfectly pseudomerohedrally
twinned. I've begun to refine my data in Refmac5 (using the automated twin
refinement), CNS (using the twin inputs) and Shelxl; I'm testing ou
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