> > No disorder is involved.
> >
> > The occupancy of an (fully occupied) atom on an n-fold rotation axis is
> 1/n
> > If a two-fold, 1/2
> > If a three-fold, 1/3
> >
> > When you sum over all the atoms in the unit cell, application of the
> symmetry operations to atoms lying on the rotation axis g
SHELXL also expects that the occupancy of a fully occupied atom on a
threefold axis should be set at 1/3, and will generate this automatically
if necessary. It will also generate automatically the necessary
constraints for the x, y and z parameters (and for the Uij if the atom is
anisotropic). I
An excerpt from the Shelx manual (which I think is a good reference for proper
handling of atoms on special positions in refinement of small or large
molecules):
4.3 Special position constraints
Constraints for the coordinates and
anisotropic displacement
parameters for atoms on special positi
On Fri, 2010-12-10 at 22:40 +, Ian Tickle wrote:
> Application of a symmetry operator to
> a point on a special position which is unchanged by the operator
> doesn't generate a symmetry copy of the point, because there is no
> symmetry copy of such a point!
Why not? Symmetry-related copy may
On Fri, 2010-12-10 at 21:53 +, Ian Tickle wrote:
> Hmmm - but shouldn't the occupancy of the Zn be 1.00 if it's on the
> special position
Shouldn't 1/3 be better for programming purposes? If you set occupancy
to 1.0, then you should specify that symmetry operators do not apply for
these atom
No that surely can't be right. Application of a symmetry operator to
a point on a special position which is unchanged by the operator
doesn't generate a symmetry copy of the point, because there is no
symmetry copy of such a point! For general Wyckoff positions it does,
for sure. If you look at
The proper occupancy for an atom on a special position depends on
how one defines the meaning of the number in that column. In the
past, refinement programs, at least I know mine did, simply expanded
all atoms in the coordinate file by the symmetry operators to determine
the contents of the uni
Good point Colin! 2-Zn insulin is of course a classic example of
this, where the two independent Zn2+ ions both sit on the
crystallographic 3-fold in R3. It doesn't matter whether you count
the metal ion as part of the protein or not: if I understand Gloria's
original question correctly, all that
On Fri, 2010-12-10 at 19:32 +0100, Petr Kolenko wrote:
> But now I have very low RMSDs. And then you read in this
> forum quite often, that we should refine against the data and not
> against the restraints. :)
Well, at 3.6A you must have low rmsds. And at 3.6A you don't really
have any data to
Hi,
Some of you were right, I did not try to modify weights. Previous
weight was 0.03 (assigned automatically), actual is 0.01 and Rwork vs
Rfree is about 0.25 and 0.33, so 8% of difference - hopefully
acceptable. But now I have very low RMSDs. And then you read in this
forum quite often, that we
Hi Ed,
> does this assume that the current folder contains only the files to be
> renamed?
Indeed it does. I was aiming to show that for simple tasks like this,
a modern shell makes things easy enough that scripts become overkill.
> Also, how does one add padding zeros?
You can just add in a
Hi,
At this resolution, such a difference in Rs could be an indicator that
the structure is over--fitted.
What weight did you choose?
Lijun
On Dec 10, 2010, at 3:17 AM, Petr Kolenko wrote:
Dear colleagues,
I appreciate any help, or any suggestion with my difficult data. Many
thanks at lea
Colin Nave wrote:
..
Also Acta Cryst. (2002). D58, 29-38 "The 2.6 Å resolution structure of Rhodobacter
capsulatus bacterioferritin with metal-free dinuclear site and heme iron in a
crystallographic `special position' "D. Cobessi, L.-S. Huang, M. Ban, N. G. Pon, F.
Daldal and E. A. Berry ( h
The other question is, you say it's 3.3Å, by which criteria ?
Xtriage might report a 4Å dataset if you take I/sigI >3 and 85% completeness
It might also make a difference which data reduction program you used.
[/Advertisement on]XDS/XSCALE or d*Trek[/Advertisement off] might squeeze a bit
more our
Ben,
does this assume that the current folder contains only the files to be
renamed? Also, how does one add padding zeros?
While Donghui didn't need zero padding, my one liner can be easily
corrected to do this in the same way Ian's is, by replacing
%d with %0nd, where n is the total number of
Assuming that your files are named something_.img what follows must
be one line):
echo | awk '{for(i=361;i<721;i++) printf "mv something_%d.img something_
%d.img\n",i+720,i;}' | bash -sf
I'd try first without piping it to bash just to make sure that it works
right.
On Fri, 2010-12-10 at 09:5
Jack (?),
On Thu, 2010-12-09 at 21:35 -0800, Jack Russel wrote:
> So is it now the time to stop further refining the solution .
R-values are not the only criteria for this. You should be looking for
a) lack of unexplained density
b) good geometry
c) acceptable R-values
This
http://xray.bmc.uu.
For anyone who is interested, I meant to include a reference to the PNAS paper
that has just come out (web-only early release) describing the wide search MR
strategy we've developed:
Stokes-Rees, Sliz
Protein structure determination by exhaustive search of Protein Data Bank
derived databases
Pr
Arnon,
We have developed an MR search mechanism which may be helpful in this scenario.
It is web accessible and available to any public or academic researchers:
https://portal.nebiogrid.org/secure/apps/wsmr/
It can use up to the full set of SCOP domains (100k) to attempt a Phaser MR
placement
Dear Petr,
An Rfree of 33% does happen, especially at low resolution. However my
experience is that with such high Rfrees there usually is some problem. The
problem might be disorder in the protein or the crystal. In this case there is
not much you can do. However, before giving up, I would at
Does one regard the metal atom in a metalloprotein as being part of the protein?
If so, a shared metal could occupy a special position in a dimer for example.
In Acta Cryst. (2008). D64, 257-263 "Metals in proteins: correlation between
the metal-ion type, coordination number and the amino-acid
Some refinement of my question:
I am working on mutant variant (point mutation, not on the interface)
of one protein already deposited in space group I432. Screw axes are
excluded, NCS operator is equivalent to missing symmetry operation.
To Fred, I always process data in P1 first. After that and
Hi Petr,
Usually IDXREF suggests more than one Bravais lattice that is consistent
with your diffraction images;
hence it is (sometimes) worthwhile trying to INTEGRATE in all possible
Bravais lattices and this allows you to eliminate a number of
possibilities (poor profiles during integration,
Quickie 1-liners are also possible in Perl, and it's a lot more
flexible than awk to boot:
perl -e 'for(<*>) {rename $_,$1.($2-720).$3 if /(.+?)(\d+)(.img)$/}'
This (as well as I suspect some of the shell scripts posted) would
fail if you had asked to rename to the range 001..360 since the
leadin
Can you exclude space groups with screw axes (I4132, I213)? It's worth trying
molecular replacement in all possible space groups to check, or try the York
Zanuda server (http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp)
Phil
On 10 Dec 2010, at 11:17, Petr Kolenko wrote:
> Dear colleagues,
>
Hi Kristof,
depending on what you termed "specific sites" the answer is definitely
yes.
I experienced such a case in the following reference related to the
AcrB structure but I remember that this situation arose also in the
case of the LTC4 structure.
-There is a baby in the bath water: Ac
Dear colleagues,
I appreciate any help, or any suggestion with my difficult data. Many
thanks at least for consideration.
I work with datasets at 3.6AA of resolution. Integrated with XDS,
scaled with SCALA. After integration and scaling in P1, POINTLESS
suggested space group I432:
Space group con
Dear,
I was wondering if anybody has experienced before the leakage of Ni-
ions (from a Ni-NTA column) and additionally binding to specific
sites in the protein structure..?
Many thanks
Regards
Kristof
--
Kristof Van Hecke, PhD
Biomoleculaire Architectu
Dear Ian,
what I see are two minima, symmetrically aranged around the special position.
One minimum is closer the molecule A, the other closer to the symmetry-related
molecule B and waters will randomly be either in minimum A, or in minimum B.
Crystal packing prevents the water from moving the p
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