A reminder about the CCP4 Study weekend 4-5 January 2014 on Complementary
Techniques.
Please note: Deadline for early bird registration is 24th November (this
Friday). After this date the registration fee increases and there will be no
student bursaries available.
Up-to-date details of
A reminder about the CCP4 Study weekend 4-5 January 2014 on Complementary
Techniques.
Please note: Deadline for early bird registration is 24th November (this
Sunday). After this date the registration fee increases and there will be no
student bursaries available.
Up-to-date details of
There are ways - the EM map is your model equiv to a PDB file and you
need to generate a set of structure factors from your map - the EM
density is put into a large box and transformed by a program such as
sfall. .
Is that possible for you? There are problems of scaling etc etc..
On 15
First Q - how good is your data - is there no possibility of twinning
or any other distraction?
Second Q - To compare those results properly we need to know how the
P2 and the P222 cell align - are the cell dimensions more or less the
same?
But the 2 plots you attach (and the list above) show
I guess you have checked that P43212 is a better match than P41212?
(And that you are running REFMAC against an mtz file with the same
symmetry as the input PDB - you may need to change the SG in the mtz
header by hand.
mtzutils hklin P41212.mtz hklout P43212.mtz
symm P43212
end
Or vice versa..
Hmm - why should a translational peak not be along the 40 axis?
Anyway othercell shows this
Conversion of cell 40, 32, 101, 90, 101, 90
can give
Laue groups
C m m m 40.0 198.3 32.0 90.0 90.0 89.60.42 [h,h+2l,-k]
Possible spacegroups:
C 2 2 21
C 2 2 2
or
C 1 2/m 1 40.0
I have a very large complex of proteins and I would like to use COOT to apply
NCS edits in the case where the “master copy” is not chain A of my complex but
any given chain.
The script that I currently use (example only, actual number of molecules is
much larger)
Dear Felix,
under Draw you can find the option NCS Ghost Control
You can change the master chain there.
Good luck!
Karsten
I have a very large complex of proteins and I would like
to use COOT to apply NCS edits in the case where the
master copy is not chain A of my complex but any
Dear CCP4 Users,
In Phenix.xtriage and phaser, the analyses of the
Patterson function reveals a significant off-origin peak that is 23.25
% of the origin peak, indicating pseudo translational symmetry at
frac. cord. vector 0.0000.5000.022 . It did not indicate any
twinng.
Dear Monica,
strong 222 rotational symmetry plus translational symmetry would give 8
molecules in the unit cell. (4 in the a.u. in P2x and 2 in case of P2x2x2x).
(test ALL options!).
Do you have models for both the ligand binding domain, or only for the DNA
binding domain? You have to search
Dear all,
i am trying to compare a set of solutions from shelxd against the correct
solution and not against the generated “unique set with sitcom my input file
looks like this:
unit_cell XXX
space_group XXX
read_sol SOLUTION 1.0 sites.pdb 18
read_set LIST 0.1 try1_fa.lst 100 18
now i tried
http://nautil.us/blog/the-math-trick-behind-mp3s-jpegs-and-homer-simpsons-face
The Math Trick Behind MP3s, JPEGs, and Homer Simpson's Face
Posted By Aatish Bhatia on Nov 06, 2013
--
===
All Things Serve the Beam
Dear All,
Does any one know how to strictly fix the cell dimensions during data
processing? In HKL2000 there is only a keyword to define the longest
vector. In XDS there is a option to input cell parameters, but sometimes
the program would not follow the input values
and switch back to the one it
Dear Niu,
It depends on which part of processing you are referring to,
i.e. the indexing step or the integration step. In MOSFLM there is no way to
enforce cell dimensions during indexing, but providing there is an indexing
solution that has cell dimensions close to the ones
Dear Niu,
OK, I did not connect this with your earlier Email. If it is
simply a case of halving one of the cell dimensions, this can be done with
iMosflm by editing the cell dimensions that come from the indexing step. This
will not affect the positions of the predictions, but
Hi Niu -
In HKL2000, you should first get an indexing solution with the 40 A
axis, as you have done previously. Then go to the tab of the GUI
labeled Macros. In the bottom row, Immediate Execution, you enter
the following:
unit cell a b c alpha beta gamma
where you replace the words
Hi all,
I got the crystal structure of a transcription factor, and every monomer
binds two molecules of the same ligand in different binding pockets. And I
also did the ITC experiment, titrating the ligand into the protein, and got
a U-shaped curve. The binding affinity for the first binding site
Dear Wei Shi,
is your ligand a small molecule? If it is a small molecule, I would
try to computationally dock the small molecule to two pockets
separately using AutoDock, and look at the estimated free energies of
binding.
Best wishes,
Tomas
On Mon, Nov 18, 2013 at 8:55 PM, Wei Shi
Thank you so much for the suggestions, Tomas! Yes, my ligand is a small
molecule. I have the crystal structure of the ligands bound to the protein,
do I still need to computationally dock the ligand to the two pockets, can
I calculate the parameters of binding directly using the crystal structure?
Hi Wei:
Based on the structure, you can calculate the binding surface between the
protein and the ligand. Maybe the two binding pockets will give you two
different numbers. And the larger one usually can have the higher binding
affinity. You also can analyse how the ligand interacts with the
Hi Eleanor,
I checked P43212 and P41212 by changing the header of mtz file and running
refmac for the same PDB input. P43212 is a better match than P41212.
Sincerely,
Dan
From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK on behalf of Eleanor Dodson
Dear All
Can anyone explain the meaning and relevance of data when the Rmerge is
100% in high resolution shell and I/sig(I) is 3.
Thanks
--
regards
Shanti Pal Gangwar
School of Life Sciences
Jawaharlal Nehru University
New Delhi-110067
India
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