It also highlights the problem with looking at plots rather than numbers
- there is still a place for them in a graphical age.
In one of the molrep outputs - the one confusingly labelled *.doc I
think - it lists each peak and its symmetry equivalents.
So I guess you would find that peak 1 is the
I'm sending this out again, as both the questions and the deadline have changed!
See email below.
Please give this some thought.
To give you a perspective, the NLS community have been emailed thus.
STFC is undertaking a fundamental re-analysis of its funding priorities, with
a view to laying
Dear Sir,
I have very little knowledge about anomalous dispersion method. The thing is
that I have just started to deal with a case of SAD. I have consulted several
text books to acquire knowledge about it though I have some queries. CCP4BB, I
think is the best place to place my questions.
Dear All,
A non-CCP4 question:
In proteins (and RNA), the term rotamer is used to refer to a specific
conformer (or class of conformers), found in structures.
According to IUPAC (http://goldbook.iupac.org/R05407.html), the term should
only apply to rotation around a single bond,
which is not
DebajyotiDutta escribió:
Dear Sir,
I have very little knowledge about anomalous dispersion method. The
thing is that I have just started to deal with a case of SAD. I have
consulted several text books to acquire knowledge about it though I
have some queries. CCP4BB, I think is the best place
This nicely illustrates the danger of using too low resolution data to
compute the SRF (I'm referring to an earlier BB discussion on this
subject, where it was suggested to cut out the high resolution data,
against, it seems to me, all rationale). You should be using as high
resolution valid data
...
2.Sometimes I found that while searching for anomalous scatterer with
SHELXD which give the coordinates of the scatterer in PDB format with
occupancy more than 1. Why anomalous occupancy may be more than 1.
Not having other wavelengths measured (in contrast with MAD
experiments), there is
No there are 6 rotational equivalent positions in R32 (i.e. not counting
the translational R centred positions which have no effect on the RF),
consisting of 2 groups of 3, call them 1,2,3 and 4,5,6. Members of each
group of 3 are internally related by the 3-fold and members of different
groups
Wikipedia is your friend!
Dispersion is defined as the change in phase velocity with wavelength
(or wave number, frequency etc), see here:
http://en.wikipedia.org/wiki/Dispersion_relation .
The phase velocity is directly related to the refractive index:
Dear Sir,
Thank you all who have replied. It is very nice to have such a wonderful
explanation of Anomalous dispersion and Anomalous scattering.
I am sorry to say that SHELXD give me the coordinates with occ 1. It is not.
Actually I am aimed to incorporate the phases from MR. During this
Thank you all who had kindly reply to me with tips. Basically I was
suggested to combine the two ligand files together, or to trick CNS to
take in my 2nd ligand file at like the prosthetic group section. The
generate.inp runs without apparent ERR message, but the refinement was
terminated with
I had thought that dispersion might be an allusion to dispersive
differences which occur between corresponding amplitudes collected at
different wavelengths due to differences in anomalous scattering. I had
explained to myself, albeit imperfectly, the apparent terminological
inconsistency
So whence the term dispersive differences between wavelengths? I believe
that is the proper term, no? Was it just a historical accident based on poor
understanding of the original meaning? I think that is the term used by some
pretty big names in crystallography.
and may have stood for
On Wednesday 22 July 2009 10:03:19 Jacob Keller wrote:
I had thought that dispersion might be an allusion to dispersive
differences
which occur between corresponding amplitudes collected at different
wavelengths
due to differences in anomalous scattering.
No. These terms were inherited
Hi,
If you're using Phaser to refine the anomalous scatterers, then their
occupancies may indeed refine to numbers 1. If everything were
perfect (data perfectly on absolute scale, f precisely correct), then
none of the occupancies should refine above one. Phaser attempts to
put the
Dear ALL:
Thanks a lot for the input about EPMR statistics. After struggling for
several days, I finally got a promising solution from Phaser with a partial
poly-Ala model with 50% completeness.
two molecules in one ASU:
solu set RFZ=4.2 TFZ=5.9 PAK=0 LLG=23 RFZ 3.8 TFZ=19.0 PAK=3
Dear Matthew,
If it is P43 and merohedrally twinned, you should not see systematic
absences for the 21 axis. In fact there is no way of getting the
P43212 systematic absences from a twinned crystal of lower symmetry.
I presume that you also tried MR in P41212.
Best wishes, George
Prof. George
Mariah,
Try ChemDraw-3D, you can draw any chemical structure conceivable and write it
out as a pdb. It can also do a wide variety of energy minimizations for you.
Best,
--Paul
--- On Tue, 7/21/09, protein.chemist protein.chemist pp73...@gmail.com wrote:
From: protein.chemist
Jacob,
In CNS/XPLOR all topology files are created equal. You are free to combine all
topology into a single file and read that into CNS. Do you have two copies of
the same ligand or two different ligands? If you have two different ligands,
you can use prodrg or xplo2d/hic-up to generate
Hi Matthew,
Recently, a colleague of mine ran into a challenging twinning problem
reported in the following publication:
Frey D, Huber T, Plückthun A, Grütter MG. Structure of the recombinant
antibody Fab fragment f3p4.
Acta Crystallogr D Biol Crystallogr. (2008), 64, 636-43
You might want to
Matthew,
Here's my $0.02:
Try more sophisticated twin tests such as xtriage from phenix or Ctruncate from
the latest CCP4 distro. Both programs include multiple twining tests. Second,
your R-factors seem very reasonable for a well refined structure missing 20% of
a not-so-well ordered
Jerry,
In similar situations, I've tried various solvent flattening approaches.
Programs such as DM allow input of a manually created solvent mask. If you
edit the mask created around your MR solution to include where you think
additional protein density should be (using for example MAPMASK
Just to add another point to look at. If there's any question about the
absences on the 4-fold, e.g. that it could be P4(2)2(1)2, then the real
space group could be P212121.
I mention this because I discussed a structure on here a while ago which
was apparently P42212, would only solve by MR
23 matches
Mail list logo
