Dear Garib,
thanks for the clarification. I'll go back to the raw data and check for split
spots at high resolution (and give Mosflm a try; initially, the data were
integrated with XDS).
Cheers,
Uli
---
dr ulrich gohlke
Dear Uli,
It seems that you are dealing with psued-twinning when cell do not overlap
after rotation with twin operator. In these case what is in one resolution on
one of the orientation becomes another resolution in another orientation of
crystals
In short:. You have an operator R that relates
Dear colleagues,
I am in the process of refining a P2(1) structure that is marked by Scala as
twinned (L-test etc.) with a twinning fraction of ca. 0.2. I am still working
on the twinning problem, so no more details about this. But what puzzles me
right now is that, if I feed the data with a m
Hi Teresa,
As Eleanor has mentioned, you should probably check out other space
groups. Xtriage gives a lot of great information and many plots to
inspect. But, if you do not know what the plots mean and just look at
the results that say the twin fraction is 0.48 you can get into some
troub
If the twin law is k,h,-l, then your a axis must almost equal the b axis?
And if the twin fraction is 0.48 then you have additional symmetry I guess?
How sure are you that the point group is P4/mmm?
On 13 March 2014 20:41, Teresa Swanson wrote:
> Dear collegues,
>
> I'm working with a drug c
Dear collegues,
I'm working with a drug complexed protein structure that is having major
twinning issues. The drug has a single Br atom on a benzene ring, which I'd
like to use for orienting the drug in the binding site. I have various
anomalous data sets, ranging from 3.0A resolution, all sca
CP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] twin refinement
Dear colleagues,
this is a request for comments on the evaluation of crystal structures that
resulted from twin refinement.
>From http://www.ysbl.york.ac.uk/~garib/refmac/Tutorials/refmac_tutorial.pdf:
"Although Rfactors are substantially
Dear colleagues,
this is a request for comments on the evaluation of crystal structures that
resulted from twin refinement.
>From http://www.ysbl.york.ac.uk/~garib/refmac/Tutorials/refmac_tutorial.pdf:
"Although Rfactors are substantially smaller with twin refinement than
without twin
refinement
Is this twinning or several crystals indexed according to different
conventions? You usually see evidence of twinning for each crystal if it is
really there..
Trigonal data can be indexed as h,k,l k,h,-k -h,-k,l or -k,-h,-l of course
so you have a 75% chance of getting the 2nd crystal on a dif
Hi all,
Thanks for the express replies. Your insights along with the article by
Prof. Garib pointed to by Prof. Pavel completes the story for me.
Regards,
ARKO
On Fri, Mar 2, 2012 at 3:09 PM, Steiner, Roberto
wrote:
> On 2 Mar 2012, at 08:01, arka chakraborty wrote:
>
> Hi all,
>
> I will like
On 2 Mar 2012, at 08:01, arka chakraborty wrote:
Hi all,
I will like to know, as a follow up of what Prof. Randy Read said, what should
be done to do the refinement against the measured data and not the detwinned F(
which refmac outputs in the mtz after twin refinement), during subsequent
refi
1) You should use measured data (after scala/aimless/truncate). In general
there may not be one to one relationship between observed data and asymmetric
unit (e.g. non-merohedral twinning) and it would not be possible to bring input
data to output file. Use original data
2) Internally refmac gro
Garib may have more to say, but the first point would be to always include the
original data file as your input MTZ file for any cycle of refinement, whether
you're using Refmac in CCP4 or phenix.refine. (In phenix.refine, if you assign
the R-free data the first time you do refinement, it will
Hi all,
I will like to know, as a follow up of what Prof. Randy Read said, what
should be done to do the refinement against the measured data and not the
detwinned F( which refmac outputs in the mtz after twin refinement), during
subsequent refinements. And also, I would like to know how to ensure
I'm worried when you say that you use the initial job's output MTZ. Refmac
replaces F with a detwinned F in the output file so you wouldn't be refining
against your measured data in the subsequent round.
Best wishes
Randy Read
Randy J. Read
On 2 Mar 2012, at 02:00, wtempel wrote:
> De
Hi Wolfram,
a few points:
- R-factors in twin refinement vs non-twin refinement are not directly
comparable:
G.N. Murshudov, Appl. Comput. Math., V.10, N.2, 2011, pp.250-261
http://www.science.az/acm/V10,%20N2,%202011,%20pdf/250-261.pdf
- did you make sure free-R flags assigned "having twinnin
Dear CCp4ers,
A good morning to everyone.
Today, I have a structure that I initially refined in space group P6522,
1mol/asu.
Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; / > 3
2.61-2.55A: Rsym=39.6%, / > 10
50.00-6.13: Rsym=6.4%
Some mild anisotropy in the resolution limits is apparent on the
Hi,
You don't say whether you've considered the possibility that the true symmetry
is higher than P61, e.g. P6122. If there's higher symmetry consistent with
your data, then either pointless or xtriage will tell you which space groups to
consider for test refinements. Another good test (if yo
Hi
i am refining a protein strucutre with space group P61. Intesity statistics
doesnot suggest any twining but refmac and phenix xtriage suggest a twin
operator with fraction 0.48. when refined with this twin operator R factors
come dowm by 3-5% and also map looks much better. but upon closer ins
Dear All
this and other fixes are on the ccp4 problems pages
http://www.ccp4.ac.uk/problems.php
Charles Ballard
On 2 Mar 2009, at 16:50, Ronnie Berntsson wrote:
I have the same problem when running the latest ccp4 (6.1.1 on os
x, updated 1 hour ago via fink). Only way I managed to circumven
I have the same problem when running the latest ccp4 (6.1.1 on os x,
updated 1 hour ago via fink). Only way I managed to circumvent it is
to add the TWIN keyword in the command file as well..
Cheers,
Ronnie Berntsson
On Mar 2, 2009, at 16:06, Carr, SB (Stephen) wrote:
Dear CCP4BB,
I have
Dear CCP4BB,
I have come across a problem when running refmac5 in CCP4 6.1.1 via the
gui. I have a twinned data set and so want to refine the twin fraction
of the data. I selected amplitude based twin refinement in the gui, but
find that the resulting command file does not contain the twin keywo
Is it true that when doing twinned refinement REFMAC does not use the
assigned FreeR set?
Eleanor
Roberto Steiner wrote:
Hi Sabine,
If your question is: Is it possible to refine twinned structures with
Refmac?
My answer is: Yes. Very well.
Best wishes,
Roberto
On 20 Feb 2009, at 16:32
>
> I used phenix to assign the free reflections putting in the twin
> operators. Doing simulated annealing in phenix, I get a rather large
> difference in R/Rfree of ~7%. Well, I guess I need to do some tweaking of
> the parameters in phenix (running the latest phenix and cci_apps). When I
> tha
Hi Sabine,
If your question is: Is it possible to refine twinned structures with
Refmac?
My answer is: Yes. Very well.
Best wishes,
Roberto
On 20 Feb 2009, at 16:32, Sabine Schneider wrote:
Hi everyone,
I got good data to 2.4A on a protein-ligand complex. I want to
solve the
structure
Hi everyone,
I got good data to 2.4A on a protein-ligand complex. I want to solve the
structure by MR using a model with 45% seq. ID and 55% similarity.
Initially the data appeared to be P622 (pointless, selfrotation function
etc). Unit cell: 145 145 65, MW protein is 28kDa
I prepared the MR mo
Dear All,
I have 1.4 A data and a molecular replacement solution for a crystal
indexed as C2, with beta approximately equal to 90. Refinement with
refmac is progressing poorly, and intensity statistics (Truncate) and
other twinning tests (xtriage) suggest pseudo-merohedral twinning with a
twin f
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