There are two different but equally good ways of indexing the reflections
in space group I213, so there is a 50% chance that your new solution and
the refined structure will be indexed differently, in which case the
phases will not agree. Also you can easily improve the experimental phases
from
Small angle x-ray solution scattering (SAXS) can also give you molecular
weight, though not quite as accurately as the best static light scattering.
While SAXS is preferably done on monodisperse systems extrapolated to infinite
dilution, cases in which the monomer and dimer are in equilibrium un
Dear
That was a quite enlightening discussion!!
I am grateful to you guys for your time!!
I will definitily try some of these to get a clear answer.
Regards
Intekhab alam
On Tue, Aug 10, 2010 at 8:38 AM, Bostjan Kobe wrote:
> Dear Intekhab
>
> Let me just add to this that gel filtration is not
Dear Intekhab
Let me just add to this that gel filtration is not an accurate method for
determination of molecular mass, because the migration on the column depends
on the shape of the protein.
The following methods can be used to determine molecular mass irrespective
of shape:
- MALLS (multi-ang
Dear colleagues,
here is one cunning plan:
to quickly evaluate the anomalous signal of a test data set with a
non-interactive script that:
1. solves the structure using SAD
2. does some solvent flattening
3. compares the resulting phases against calculated phases from a
refined, isomorphous struc
Hi Pavel:
Thanks a lot! I found it in the latest version of phenix, and it works well!
Best Regards, Hailiang
> Hi Hailiang,
>
> yes, phenix.maps tool (command line) can compute any number of regular
> kFo-jFc or sigmaa weighted kmFo-jDFc maps, where k and j are any
> user-defined numbers. The
To determine the oligomeric state of a protein (monomer or dimer in your
case), it's useful to use the PISA server. You upload your pdb file from
the crystal structure.The server calculates the areas of interfaces
(buried area) and deltaG (change in Gibbs energy) upon oligomer
dissociation. (E
Hello Intekhab,
Your results do not seem surprising at all. It is not uncommon for molecular
interactions such as dimerization to be more stable at lower temperatures, and
this is exactly why you are seeing the shift to higher elution volumes at lower
tempratures. At lower temperatures, both th
Hi Hailiang,
yes, phenix.maps tool (command line) can compute any number of regular
kFo-jFc or sigmaa weighted kmFo-jDFc maps, where k and j are any
user-defined numbers. The maps can be output as in various formats (MTZ,
Xplor/CNS, CCP4). B-factor sharpening can be applied.
The sharpening
Hi there,
Does phenix have any utilities which can do B-factor sharpening (with
user-specified Bsharp values) when calculating maps? Thanks!
Best Regards, Hailiang
On Monday 09 August 2010, Tim Gruene wrote:
> Dear Rex,
>
> I am not sure what exactly you are looking for, but why don't you start with
> the
> Refmac documentation? Item 3 probably corresponds to a single TLS group in
> refmac.
That is not quite correct.
An overall anisotropic B term is a
Rakesh,
Composite maps are used in publications some times however many folks also
publish the 2Fo-Fc or even better the 1Fo-Fc. These can be obtained by
selecting a button in refmac to export the maps and then visualize them in
pymol.
Scott
On Mon, Aug 9, 2010 at 8:37 AM, Rakesh Joshi wrote:
Hi all,
I wanted to know the best way to make a composite file using ccp4.
I have tried the SF-check program GUI; but it does not give me an option to
construct composite maps.
Also, is it true that when one does molecular replacement, if one wants to show
an electron
density map in a publicati
Dear Rex,
I am not sure what exactly you are looking for, but why don't you start with the
Refmac documentation? Item 3 probably corresponds to a single TLS group in
refmac.
Or maybe you could specify what you mean by "the use of [...] in ccp4".
Cheers, Tim
On Mon, Aug 09, 2010 at 02:26:12PM +0
Can anyone supply information on the use of the following in ccp4:
1. Bulk-solvent correction
2. Refinement of individual isotropic B-factors
3. Refinement of an anisotropic overall thermal parameter
Rex Palmer
Birkbeck College, London
*The "International Conference on Antivirals for Neglected and Emerging
Viruses" (ICAV-9) will take place in the historic capital of the Hanse,
Lübeck, Germany, from October 10 to 13, 2010*
Dear colleague,
Infectious viral diseases exert a shocking toll on the developing
world. Over 2.5 mill
Hi everyone
Sorry for some non specific query!
i am working with a protein that shows a dimer in the crystal structure but
when i tried to figure out that with standard molecular markers in gel
filteration (superdex-200, 24ml column) it turned out to be a monnomer.
Native gel analysis after in
Hussain Bhukyagps wrote:
Dear all,
i want to know that how can we find Rmerge from the refinements done
in CNS..??
Hi,
I think you have the terminology wrong: Rmerge (or Rsym nowadays when
most diffraction data is recorded from a single crystal) is provided by
the data frame diffraction s
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