Hi Yarrow,
That solution looks very reasonable to me.
If you are worried about the size of your doughnut-hole, look at the
packing of the latest structure we solved. :)
https://dl.dropboxusercontent.com/u/5116503/4J05.png
best
-Bjørn
--
Bjørn Panyella Pedersen
Macromolecular Structure Group
D
Dear Yarrow
your toroidal structure suggests that the protein may actually have the
propensity to assemble as such in solution, hinting a connection to a
biologically relevant state. Do you have any experimental information that it
does so? e.g. via SAXS, MALS, native PAGE etc.?
best regards
Very reasonable structure, I guess in the direction perpendicular to your
picture you will have next donut etc.
You can call this - nan-pore ;-)
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnology
Tel Aviv University 69978,
How pretty - I love circular molecules!
Eleanor
On 19 March 2014 15:58, Yarrow Madrona wrote:
> Thank you to everyone for their input. I am posting a picture to some of
> the symmetry related molecules shortly. There are six dimers related by
> symmetry (60 degrees) with a "donut" hole in the m
Hi,
First, there is nothing magical about contouring a map at 1 rms.
The standard deviation of the electron density values really has no
relationship to the rms of those values, and appears to generally be
much smaller. This is discussed quite brilliantly in the recent paper
http://www.ncbi.n
Before putting in the ligand, there is a clear density for three extra
atoms at more than 3 sigma in the Fo-Fc map but for other atoms the density
appears around those 3 peaks in the 2Fo-Fc map only and not in the Fo-Fc.
Thanks for your reply.
Amit
On Wed, Mar 19, 2014 at 8:57 PM, Sampson, Jared
Thank you to everyone for their input. I am posting a picture to some of
the symmetry related molecules shortly. There are six dimers related by
symmetry (60 degrees) with a "donut" hole in the middle. This was troubling
to me as I have solved mostly tighter packing structures (monoclinic or
orthor
Hello,
My protein is 26 kDa and the resolution of the data is 1.90 angs. My ligand
is 174 Daltons. and it was soaked into the crystal. Ligand is colored and
the crystal after soaking takes up intense color. However if we soak more
than optimum, the color deepens in intensity but the crystal diffra
Yes in the first couple of rounds of refinement it refines very well for a
3.2 angstrom structure (Now at 30%/24% Rfree/R). Everything Packs
contiguously except for a "donut" hole in between six dimers that are
related by symmetry. Trying to put a molecule there disrupts the symmetry
and leads to c
Applications are now open for the BCA/CCP4 Summer School in Protein
Crystallography to be held at Diamond (UK) from Tuesday 26th August to
Sunday 31st August 2014. Applications close 1st May 2014. References are
due by 8th May 2014.
The BCA/CCP4 Protein Crystallography Summer School is intende
You can have a look at the pair_fit function in PyMOL (see
http://www.pymolwiki.org/index.php/Pair_fit)
Cheers
Jose
On 19/03/14 08:34, sreetama das wrote:
Dear All,
Is there a way to superpose multiple, discontinuous
stretches of residues between two protein chains ?
Dali
Dear CCP4 users,
I am doing a molecular replacement with Phaser and I am using more than one
ensemble for the search. How could I, once that one of them has been
placed, fix it as a solution in order to be able to provide an additional
fragment for further MR search?
I have a second doubt about s
Dear Sreetama,
For this, Gesamt from ccp4 should do the work. Run gesamt without parameters to
get instructions, they are basically the same as for ccp4's superpose.
HTH,
Eugene
On 19 Mar 2014, at 07:34, sreetama das wrote:
Dear All,
Is there a way to superpose multiple, discont
didn't know about the trick to move the pointer (and for some reason it doesn't
work on my computer at home but does at work).
and yes, editing pdb files by hand has to be done carefully - however, I find
that editing the pdb file (before refinement), is sometimes the quickest way
for me, and t
In this case, editing the pdb file is probably the best approach. However, my
favorite approach is "Validate" "Difference Map Peaks". By pressing "." (next
peak) or "," (previous peak), one can quickly go through all problems (red
density) or unexplained peaks (green density). The pointer will
Dear All,
Is there a way to superpose multiple, discontinuous stretches of
residues between two protein chains ?
Dali output shows that there are discontinuous stretches between the PDBs that
are being aligned. But I can not find any option to download the superposed
PDB. The outpu
I think you have solved it! That is an excellent LLG and if you can't see
anything else in the map, then there s prob. not another molecule.
Does it refine? If you look at the maps following refinement any missing
features should become more obvious.
Solvent content of 65% is not uncommon.
Elean
17 matches
Mail list logo
