Dear SDY,
It is impossible to deduct from data statistics alone the difference
between e.g. P43 21 2 and P41 21 2. Also with weak data like you have, a
lot of artifacts may arise due to (weak) ice rings, intensity from
neighboring strong reflections getting into the integration boxes of
weak
Dear all,
What's the difference between no prior phase information, phase and
FOM, Hendrickson-Lattman coefficients, and SAD data directly in the
refmac5 GUI of CCP4i?
I have a SAD dataset and solve the phase by phenix.autosol. Now I want to
refine the structure by refmac5, which kind of input
Dear all,
I am now determining a structure at 2.2 A resolution. The space group is
C2, and there is only one molecular in an ASU. During the refinement, some
weird electron density appears right on the two-fold axis. Does anyone have
any idea what could this be? Thanks a lot.
Best regards
Dear all,
I am now determining a structure at 2.2 A resolution. The space group is
C2, and there is only one molecular in an ASU. During the refinement, some
weird electron density appears right on the two-fold axis. Does anyone have
any idea what could this be? Thanks a lot.
Best regards
Am I worrying about something unnecessarily?
I have several protein-drug datasets, all in the same spacegroup, but wildly
varying resolutions.
I wish to use the same reflections for calculating R-free in all cases.
Using xia2 with a reference dataset for both indexing and R-free seems to work
Dear Yogesh,
Since your difference density is at the center of a hexamer, you might
be looking at the 6-fold average density of one or two fatty acid
molecules. Just try to fit one and generate to other 5 equivalent
molecules and look if this makes sense.
Otherwise, I agree with Mark that with
It might be a 50% occupied protein side chain(s), since only one of the
two equivalent protein side chains can occupy this position.
Best,
Herman
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Crystal Xu
Sent: Monday,
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Dear Shutong Xu,
one often finds artefacts on special positions. As far as I
understand, these are numerical 'instabilities' or artefacts rather
than of chemical origin.
Best,
Tim
On 11/05/2012 10:50 AM, Crystal Xu wrote:
Dear all,
I am now
Yes, if your data does not extend to high resolution, your free
reflections will not extend to high resolution either (e.g. are not
observed).
Herman
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Antony Oliver
Sent:
Hi Antony,
Using xia2 with a reference dataset for both indexing and R-free seems to
work fine, apart from the fact that the resulting mtz file, now contains
R-free labels for reflections that have no observations… i.e. taken from the
higher resolution reference dataset; see output below.
As only small part of the molecules is shown and it appears to be in
poly-alanine representation, more interesting
thing may happened apart of numerical instabilities of Fourier transform.
These can be mutually exclusive conformations that brake local symmetry but
preserve overall symmetry.
The
There are several questions here.
1) What is the point Group - P4 or P422.
I find the pointless statistics which check all symmetry operators singly
useful. If the 2 fold kh-l gives about the same CC as the 4 fold operators k-hl
-h -k l -k h l then you probably do have point group P422. ( But
Dear Cai
On 5 Nov 2012, at 09:46, Qixu Cai wrote:
Dear all,
What's the difference between no prior phase information, phase and FOM,
Hendrickson-Lattman coefficients, and SAD data directly in the refmac5 GUI
of CCP4i?
I would use SAD data directly if you have SAD data set. It just
I don't know what exactly the phenix.autosol output is.
If you are satisfied with the solution and have a mtz file containing F sigF
HLA etc, then use Hendrickson Lattmann coefficients.
If there is only Phase/Fom then use that.
I am not sure how you would fare with SAD data directly..
But
Just give CAD the resolution cut off of the new data set..
Eleanor
From the CAD documentation..
RESOLUTION [ RESOLUTION OVERALL dmin dmax ] | [RESOLUTION FILE_NUMBER i
dmin dmax ]
Use either:
RESOLUTION OVERALL dmin dmax
for overall resolution limits, or:
RESOLUTION FILE_NUMBER i dmin dmax
to
Any spurious blob on a symmetry axis is multiplied up of course.
And when you finish building side chains it may reduce in size.
But waters etc can sit on special positions - you just enter them with occ =
0.5 and refine as usual..
Eleanor
On 5 Nov 2012, at 09:49, Crystal Xu wrote:
Dear
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If you want to remove the indices which are not observed, you can use
sftools (this has been suggested to me on this board, sorry I do not
remember by whom).
sftools eof
read yourfile.mtz
select only column IMEAN present
write temp1.mtz
END
eof
mv
Thanks Eleanor - guess I should have plumbed the depths of the CAD manual a
little further.
Works perfectly.
Antony.
---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ
I am not sure how you would fare with SAD data directly..
If you would like a comparison, check out the refmac paper.
http://journals.iucr.org/d/issues/2011/04/00/ba5152/index.html
See Figure 1 - this shows model building with ARP/wARP on over 100 data
sets using
the different Refmac
It might be a 50% occupied protein side chain(s), since only one of the
two equivalent protein side chains can occupy this position.
Best Herman
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
On Behalf Of Crystal Xu
You know what? Scratch what I said. As Mark says, there isn't any 2Fo-Fc
density, which is suspicious.
However, I would still model what may fit in it, with appropriate
occupancy, based on the symmetry. To be doubly sure.
I have, in the past, used
Dear Rana,
I think you need to clear up some confusion about this experiment. MBP fusions
suffer from a number of drawbacks depending on what you are doing. First, did
you use the MPB domain to purify the fusion protein (with an amylose column)?
If so, you also purified native MBP from the
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Dear,
from the lack of any shelxc-related output in the log-file my first
guess is you don't have shelxc installed on your system - do you? It
is not part of ccp4 and must be installed separately.
Thanks indeed Eleanor, when I get a moment I will add this too to the xia2
cad script!
Best wishes,
Graeme
On 5 November 2012 11:37, Antony Oliver antony.oli...@sussex.ac.uk wrote:
Thanks Eleanor - guess I should have plumbed the depths of the CAD manual
a little further.
Works perfectly.
Dear Sir Tim
from the lack of any shelxc-related output in the log-file my first
guess is you don't have shelxc installed on your system - do you? It
is not part of ccp4 and must be installed separately.
I have already have installed shelxc/d/e on my computer and its also
shoeing in CCp4 program
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Dear Shanti,
to track the problem I suggest you download the tutorial and data from
my homepage at
http://shelx.uni-ac.gwdg.de/~tg/teaching/anl-ccp4/index.php and run
shelxc outside ccp4.
If that works, one can further try to isolate the problem. Is
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