Dear Wei,
It seems that coot detects some discrepancies between cif file and your
ligand. It is not uncommon that the program used to generate your ligand
pdb produces atom definitions that are not correctly read by programs
used to generate restrains, such as PRODRG. In order to overcome the
Dear All,
izit dye is a solution containing methylene blue that you could prepare
in your lab. I usually prepare a solution of 0.05%w/v of dye in water
and then I add a volume of dye solution equals to 10% of the volume of
the drop containing the crystal to test. I prefer to add the dye
solut
Dear Swastik,
izit dye is a solution containing methylene blue that you could prepare
in your lab. I usually prepare a solution of 0.05%w/v of dye in water
and then I add a volume of dye solution equals to 10% of the volume of
the drop containing the crystal to test. I prefer to add the dye
s
Dear all,
I am using xds (with graphical interface xdsgui) to process several
diffraction data of a membrane protein that I have crystallized. At the
end, I run XDSSTAT in order to check the statistic parameters of the
process and my attention is captured by the R_d plot: R_d drops during
the
Dear Mahesh,
In addition to RMSD plots, you could try to quantitatively analyse the
protein residue flexibility in order to detect backbone conformational
transitions by means of the method proposed in:
Local Fluctuations and Conformational Transitions in Proteins
Rocco Caliandro, Giulia Ross
Dear Andre,
you could try with the protocol described in the following paper
Acta Crystallogr D Biol Crystallogr. 2013 69,920-3.
Using high-throughput in situ plate screening to evaluate the effect of
dehydration on protein crystals.
Douangamath A, Aller P, Lukacik P, Sanchez-Weatherby J, Morae
Dear all,
I am working on a membrane protein covalently bound to a molecular
antanna: it is known that this molecule binds to lysine residue but I do
not know how many and which lysine residues it binds. 20 diffraction
datasets of this protein-ligand complex have been obtained and now, I
wo
Dear Afshan,
Maybe what I suggest you have already tried: have you tried to fit a
citrate molecule? The blob seems to be branched, thus compatible with
such organic molecule.
Danilo
On Thu, 12 Dec 2013 03:34:07 -0800, Afshan Begum
wrote:
Dear Experts,
I collected a data set (1.12A) of on
Dear Rongjin,
I think that HADDOCK (http://www.nmr.chem.uu.nl/haddock/) is the best
solution for your requests.
Danilo
On Tue, 7 Jan 2014 16:36:43 -0500, rjguan wrote:
Dear All,
We have a RNA binding protein with structure known. We want to dock a
RNA molecule to
the protein structure, and
Hello,
it is not the first time that I see such electron densities near to His
residue.
However, in my structures (3N30, 3N32), I was sure that Zn, Pt or other
metals were present in the crystallization condition.
You have tried to refine with Zn rather than Mg that seems to be present
in the
Dear Meisam,
In the past I had similar problems, because of jligand and other cif
generators can make errors when generate cif files, as it has been
written before. I have solved these problems by using sketcher (ccp4)
and PRODRG server (http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg).
I u
Dear Almudena,
You can try to run XDS with 300 frames. At the end, you have to open the
file called INTEGRATE.LP and copy the refined value of
REFLECTING_RANGE= REFLECTING_RANGE_E.S.D.=
BEAM_DIVERGENCE=BEAM_DIVERGENCE_E.S.D.=
at the end of your XDS.INP.
Now, you can re-run XDS with all
Dear Bing Wang,
To solve your problem, you may try to take a eme ligand directly from a
PDB that contains it, e.g. 1HRC.
You should download the PDB file and to copy and paste the ligand
coordinates in a new file and then use this new pdb file to refine your
structure.
It could be a good s
Dear all,
I am Dr. Danilo Belviso and I am working on a platinum-based inhibitor
for matrix-metallo proteasis.
I have obtained the crystal structure of the adduct Pt/protein and, for
me, would be very interesting to know the cavities of the protein within
the crystal, namely by considering
Hi! Does anybody know which is the range is used by REFMAC to vary bond
distances, angles, and torsions of a ligand molecule during a refinement
process? Is it possible to control and choose this range? In which way?
Where are these information in cif dictionary obtained by sketcher in
CCP4?
t
Hello everybody,
I am working with a protein that should be covalently bound to an
organic ligand and I would calculate the correlation coefficient of this
ligand both against 2Fo-Fc and Fo-Fc map arising from refining (map
calculated in the presence of ligand).
To do this, I am using OVERLA
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