Jeremy, apparently I was unclear (and possibly moving off-topic) since I
got other emails off list about this. I did not mean to imply that I would
use Ramachandran restraints to fix a register error since this obviously
needs to be addressed in real space. Rather, inspection of the
Ramachandran
Hi
I have a protein with two substrate. when I am doing the binding studies
with the two substrate separately, I am finding one of the substrate to have
similar kd and Km. however the km and kd values are almost 30 fold different
for the other substrate. it binds 30 fold more tightly then
Doesnt pisa give you some of this information? It lists all likely
homodimers and I think gives RMSD too
Eleanor
On 24 February 2015 at 22:00, Thomas Holder thomas.hol...@schrodinger.com
wrote:
Hi Dan,
gaps/insertions should be no problem for PyMOL's rms_cur command, as long
as chain
Dear All
We have a vacancy for an enthusiastic postdoctoral researcher to join our
group within the Research Complex at Harwell to investigate the structure and
function of a novel bacterial integral membrane complex involved in innate
immune evasion using primarily single particle electron
Dear CCP4 Users,
CCP4 Core Group would like to estimate the demand for 32-bit Windows
distribution of CCP4 Release 6.5.
Therefore, could you please help it by replying to this e-mail without
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No, the question seems to be slightly different. While one can use
either CCP4's SSM or GESAMT to superpose 2 dimers, these algorithms
would balance RMSD between both chains and produce something optimal for
both chains. What is required, however, is optimal superposition on one
pair of chains
Oops, sorry: lsqman gives you the rmsd between pairs not moleman.
Additional comment: PDBSET should also give you the rmsd between B1 abd B2
using the coordinates generated by lsqman.
Phil Philippe BENAS, Ph.D.
X-ray diffraction and computing facilities manager
Laboratoire de Cristallographie et
Dear CCP4bbers,
If I remember correctly you can do this in LSQMAN (EXPLICIT superimposition
command if I remember well): the superimposition is made between residues of
chain A2 onto those of chain A1, then you apply the rotation/translation to all
the A2B2 dimer and moleman gives you the rmsd
Hi Adam,
The diffraction improved from 8 Angstrom to 2.6 Angstrom. But, I had also
removed the His-tag from the protein, so I am not sure how much was the
role of this step and how much was it because of the addition of DTT. Two
variables in one experiment :).
-Gyan
On Wed, Feb 25, 2015 at
I think the Ramachandranplot should be used in the refinement and
rebuilding process - a Ramachandran outlier is a flag that that region of
the model needs a closer look, and the fix may be more complicated than
simply rotating a peptide. Maybe a C-beta is pointing the wrong way, maybe
there is a
Hello everyone
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Dear Crystallographers,
May be this is a very stupid question- which terminology should we use for
crystal data collection- Crystal Rotation or Crystal Oscillation or
both?
I apologise if this is already discussed!
Best,
Dipankar
--
Dipankar Manna
Research Scholar
Department of Chemistry
Applications are invited for a PhD studentship co-supervised by Dr. Harry Low
and Prof. Martin Buck at Imperial College, London (South Kensington campus),
starting from October 2015.
Using a hybrid methods approach consisting of X-ray crystallography, electron
microscopy and cell biology, the
To give a short practical rather than a lengthy philosophical answer:
- in real space: you can try Ramachandran restraints or secondary structure
restraints -- indeed, both can be switched on in Coot in the refinement and
regularisation parameters window (R/RC button in the top right corner).
Hi
The Rotation Method in Crystallography ed Arndt Wonacott uses both crystal
oscillation and crystal rotation.
However, most of the time these days we don't oscillate the crystal when we're
working at synchrotrons, but occasionally do when working in the lab.
On 26 Feb 2015, at 09:34,
Hi,
Sorry, can’t take the credit for that! The names that come to mind are Gerard
Kleywegt and Alwyn Jones.
I’ve actually said in the past that, the more criteria you add to optimising
your model, the less likely that you can satisfy all the criteria and still
have a wrong model! But I
I saw several excellent remarks about Ramachandran plots come by, but
the main points still seem missing, I think.
Phi and psi are not fixed parameters with limited freedom like angles,
bond lengths or planarities. By keeping a certain bond lengths
restrained at, for example, 1.543+/-0.021
Hello Ulrike,
In addition to other answers, one of the more esoteric (but surprisingly
effective) ways to destroy the protein 'skin' on drops is to add a tiny bit
of Trypsin solution. Crystals generally tend not to be affected, but (at
least in my experience) the protein skin dissolves within a
On Feb 26, 2015, at 4:51 PM, Srivastava, Dhiraj dhiraj-srivast...@uiowa.edu
wrote:
Hi
I have a protein with two substrate. when I am doing the binding studies
with the two substrate separately, I am finding one of the substrate to have
similar kd and Km. however the km and kd values
Dear Kevin
Please re-read my earlier email paying particular attention to the words
explicitly
and expressly. To my mind, the notion of moving a Ramachandran outlier by
moving
a dot across a graph (which you feel is a danger) is identical to expressly
forcing that
residue into a favoured
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