found for SG
> P212121 it is surprising if the refinement works better in P222!
>
>
> But check how the refinement and map generation is done. If the PDB file
> defines the SG as P212121 then maybe the refinement assumes the mtz file
> should also have that symmetry..
>
Hi all,
I am working with a protein-ligand complex structure. The data was indexed
with XDS and mtz file is generated using Phenix---Reflection
tools---Reflection file editor. The space group used was P222. Then, I used
the Phenix---Molecular replacement to find a solution (try all possible in
same
PM, Wei Shi wrote:
> Thank you so much, Nigel! I will try as suggested.
>
>
>
> On Wed, Aug 20, 2014 at 5:17 PM, Nigel Moriarty
> wrote:
>
>> Wei
>>
>> I ran your SMILES string in the latest version of eLBOW and generated the
>> attached file which ha
Thank you guys so much! Fixed!
Best,
Wei
On Wed, Aug 20, 2014 at 4:13 PM, Christian Roth <
christian.r...@bbz.uni-leipzig.de> wrote:
> Hi Wei,
>
> have you supplied a valid pdb file? That is the mentioned missing
> parameter.
>
> Cheers
>
> Christian
>
>
&g
e using version 1.8.2 which is from Feb 2013. I suggest you upgrade
> your Phenix installation to 1.9 (or a nightly build) to obtain all the
> great new features.
>
> http://www.phenix-online.org/download/nightly_builds.cgi
>
> Cheers
>
> Nigel
>
>
> On Wed, Aug 20,
5 287549;
> Fax (+44) 1865 287547
> Email matth...@strubi.ox.ac.uk
> Website http://www.strubi.ox.ac.uk
> -
>
>
> On 8/20/2014 3:45 PM, Wei Shi wrote:
>
>> Hi all,
>> I am working on solving a X-ray crystallographic protein-ligand
>>
Hi all,
I am trying to display F0-Fc omit map in PyMol. I got the mtz file from
Phenix, and now use CCP4i FFT to generate the map for PyMol. I followed the
instructions from the below link:
http://www.p212121.com/2010/04/26/display-a-mtz-file-in-pymol/
And, I constantly got the following error me
Hi all,
I am working on solving a X-ray crystallographic protein-ligand structures.
Attached please find initial oleoyl-CoA structure (elbow.001.pdb) and the
ligand structure in the final model (ligand in structure.pdb). When open
these in pymol and use "show as lines and set valence, 0.1" to show
D=37
>
> Best regards,
> Tim
>
> On 03/04/2014 04:48 AM, Wei Shi wrote:
> > Dear all, Does anyone happen to know examples of 2 ligands bind to
> > a single protein / each monomer protein in 2 different ligand
> > binding pockets? I know the following example: (1).
>
Dear all,
Does anyone happen to know examples of 2 ligands bind to a single protein /
each monomer protein in 2 different ligand binding pockets?
I know the following example:
(1). phosphofructokinase, which binds ATP as both a ligand and a feedback
inhibitor in different sites
(2). 2 cAMP bound t
s around with the view/colors of course.
>
>
> Hope this helps
> Folmer
>
> ps: there's actually a PyMOL bulletin board :-)
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
> 2014/1/20 Wei Shi
>
>> Hi all,
>> Please see attach
epeating the same for
> the second binding site. This will give you a better idea of which site is
> high affinity one.
>
> Hope it works.
> Monica
>
>
> On Tue, Nov 19, 2013 at 7:25 AM, Wei Shi wrote:
>
>> Hi all,
>> I got the crystal structure of a t
important and should be mutated first? Thank
you so much!
Best,
Wei
On Wed, Dec 11, 2013 at 10:31 PM, Wei Shi wrote:
> Hi guys,
> Thank you so much for the suggestions! I used DSXONLINE to rank the two
> binding sites according to binding free energy and get the prediction
> the
ons after you refining
> > >> >> the structure. These things may give you some hints about which
> > >> >> binding site is more strong.
> > >> >>
> > >> >> Dee
> > >> >>
> > >> >>
> > >> >&g
?
Best,
Wei
On Mon, Nov 18, 2013 at 9:03 PM, Tomas Malinauskas <
tomas.malinaus...@gmail.com> wrote:
> 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 AutoDoc
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 i
pdb for the protein plus the mtz file onto Coot.
3. Now, in coot, I could move the ligand to fit the density by 'real space
refine zone'.
Thank you so much!
Best,
Wei
On Mon, Oct 7, 2013 at 7:43 PM, Wei Shi wrote:
> Hi all,
> I was solving a protein-ligand complex structure and
Hi all,
I was solving a protein-ligand complex structure and got a molecular
replacement solution with the protein as the search model and now trying to
fit the ligand to the electron density in coot. It seems that the ligand
needs to change conformation to fit the density well.
So, I created the
Hi Dr Afonine,
Thank you so much for the reply!
I also posted on Phenix mailing list and Dr Nathaniel Echols suggested me
to turn on X-ray/stereochemistry weight optimization (for non-GUI users,
optimize_xyz_weight=True).
So, I ran the refinement again with default settings + Rigid body+
Simulated
Hi all,
I have a refined structure with phenix. The resolution=3.2 Å. After
refinement, the R-work=0.2186, R-free=0.2864, Bonds=0.010, Angles=1.515.
Ramachandran outliers: 4.8%, Ramachandran favored: 80.8%.
Rotamer outliers: 14.5%, c-beta outliers: 2
clashscore: 16.28, overall score: 3.32
To fi
Hi guys,
I was trying to view the simulated annealing omit map generated by Phenix
in Coot. When I opened resolve_composite_map.mtz and *_ed.pdb in Coot, I
could only see one monomer of the protein. It should be two dimers of the
protein plus two pieces of DNA. And when I opened the *_ed.pdb in pym
Hi all,
I was trying to solve the structure of a protein in several different
datasets using xds and phenix. I could solve the structure from one dataset
in space group P4. For another dataset, I could solve the structure using
the monomer of the structure I got from the first dataset as search mo
Hi all,
I am working on solving the crystal structure of a protein-DNA complex. I
could complete one strand of the DNA to fit the electron density using
Coot, but for the other strand, the density for several bases at each end
of the DNA is not clear and it's missing several bases at each end of th
Hi all,
I am refining a structure of protein-DNA complex with coot. The DNA in
my search model is shorter than the DNA in the crystal, and now I
could see the density for extra DNA(6 base pairs) on either end of the
search model DNA. But, I don't know how to build the extra DNA back to
fit the dens
Hi all,
I have been trying to solve a protein-DNA complex structure using molecular
replacement. I suspect two copies of protein bind one piece of the DNA, and
the angle between the two copies of protein is somewhere between 130 to 180
degrees. I could get molecular replacement solution using a se
Hi all,
I want to change a piece of DNA in pdb file to match the target DNA
sequence in order to be used as a search model in molecular replacement.
Does anyone happen to know how I could do this? Thank you so much!
Best,
Wei
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