Structure calculation of biomolecules by NMR relies on unambiguous assignment
of all protons in the biomolecule so as to get enough inter-proton distance
contraints (from NOEs). Two protons that are in close proximity (less than 5
ang) through space will have a dipolar interaction that is manif
There are about 20 structures solved by NMR with chain lengths above 300
residues. Some of them are solved by combination of restraints and modeling
(e.g. 2010 Nature paper describing implementation of Rosetta modeling
coupled with backbone-only data, by Raman/Montelione/Baker et al.).
Principal p
Dear members,
I know that it is not possible to solve a structure by nmr of more than
approx. 30 kda. But I have to admit that I dont know why. What exactly is
overlapping?
With best regards,
Lena
The most extreme degree of confusion (or at least of requirement for fast
mental arithmetic) I have come across in relation to this topic is the habit
of small-molecule crystallographers working on accurate density studies to
characterise the resolution limit of their datasets by quoting the maximu
This has been a point of confusion
Here are the conventions used in a few of the classic SAXS text vs. recent
reviews:
--
I believe Guinier actually used the variable "u" in his thesis, but must have
changed at some point (I don't have it handy to check at the moment).
Guinier & Fo
You can do this with PyMOL with the supercell script:
http://pymolwiki.org/index.php/Supercell
Cheers,
Thomas
On 06/30/2011 02:52 PM, Hargreaves, David wrote:
Does anyone have a rigorous method (or script) for generating an
extended lattice e.g 3x3x3 unit cells from any pdb file?
Any help gr
PDBCur (CCP4) should be able to generate the unit cell at once, which then
should be translated to 3x3x3 "cube". All may be done within a single run of
PDBCur, a simple keyword input is required. Same job is doable with PDBSet.
Eugene
On 30 Jun 2011, at 15:36, Petr Leiman wrote:
> Apologies fo
Its obviously not going to be possible to give a unique
chain letter for every chain in 27 cells, but forget renaminmg
the chains and its very easy to generate the models to look at-
might even do it in a triple-nested foreach loop in csh.
After generating the whole cell as suggested by David or E
Apologies for suggesting a non-CCP4 solution, but UCSF Chimera can do that and
more (interactively!):
Tools -> Higher Order Structure -> Unit cell
Petr
On Jun 30, 2011, at 2:52 PM, Hargreaves, David wrote:
>
> Does anyone have a rigorous method (or script) for generating an extended
> latti
As well as pdbset, you can use pdbcur. A combination of keywords genunit, symop
and symcommit.
I’d probably use genunit (applicable to whatever spacegroup you have), followed
by a second call using symop/symcommit to apply unit cell translations.
Cheers
Martyn
From: CCP4 bulletin board [mailto:
Well - you have a problem of chain IDS,
but pdbset xyzin asymm.pdb xyzout whole-cell.pdb
symgen P212121 (say)
end
will generate a whole unit cell,
then
pdbset xyzin whole-cell.pdb xyzout whole-cell-+100
symgen x+1,y,z
end
etc
will move that unitcell.pdb
You would have to put them all together
Hi Dave,
as first step you apply all symmetry operators of the space group to the
pdb-file in order to fill the unit cell, and store all copies in the same
PDB-file. You can do this with pdbset and the symgen keyword, see
http://www.ccp4.ac.uk/dist/html/pdbset.html#symgen
Check with coot that all
Does anyone have a rigorous method (or script) for generating an
extended lattice e.g 3x3x3 unit cells from any pdb file?
Any help gratefully received,
Dave
David Hargreaves
Associate Principal Scientist
_
AstraZeneca
DE
On 30 Jun 2011, at 01:42, Michael Thompson wrote:
> the introduction of a disulfide can create artificial "crystal contacts,"
> which also aid in crystallization
Another example of this is described here:
The structural and energetic basis for high selectivity in a high-affinity
protein-protei
Hi James,
Well, I think there's q (or s) which depending on where you're coming
from can be 4*pi* sin(theta)/lambda, or 2*sin(theta)/lambda, or . *
sin(theta)/lambda) or or * sin(theta)/lambda.
Small-angle X-ray scattering (and other fields) uses those as symbols
for the momentum
On 06/29/2011 10:22 PM, Paul Lindblom wrote:
Hi everybody,
can anybody tell me how crystal contacts are defined? Are there good and bad
crystal contacts? They are the most important interactions with impact on
the crystal quality, but they are not of covalent nature, aren´t they?
With best rega
Hello All,
Is there precedent or a conventional shorthand (e.g. greek letter) for
sin(theta)/lambda?
Thanks in advance for any help or suggestions.
James
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