Dear all,
I am new to the CCP4 program for structure determination.
Now I am trying to solve a complex structure with 2.5A resolution.
I refined the structure with Refmac5 and built the model also using coot.
Now I'm trying to insert the ligand molecule into the active site
of electron den
Hello, ccp4,
I'd appreciate any comments on modeling softwares you would recommend
particularly in these aspects:
1) the capability of modeling any given aa sequence;
2) user-friendliness;
3) cost, etc
There are packages such as Modeler, Quanta, Insight II, but these are quite
expensive. I have
Yes, this is an inconsistency between the version of the Phaser executable
and the version of ccp4i. To get around the problem that filenames,
particularly in Windows, can have spaces in them, the ccp4i GUI now wraps
filenames with quotation marks. But this required a corresponding change in
th
Frank,
You will get a variety of opinions here, but I really like my Olympus
SZX-12. (I used many different models when I was training, and I by far
preferred the Olympus scopes for their ergonomics. YMMV) For
xtallography you will want a separate (cold) light source with fiber
optic cable. I hav
It appears that CCP4i is accessing an older version of Phaser, which
will generate this error. Phaser 1.3.3 is current for CCP4 6.0.2. I had
a similar problem when I had a stand-alone install of Phaser and later
upgraded to a CCP4 package that contained its own version of Phaser. I
think you have t
Your ligand may well be MTQ or MTV whcih already
exists in the PDB
(MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(V)
S
/ \
this has the peterin Mo(S)(O2)
\ /
S
you can download the dictionary connectivity from
either
I think you can do what you want using elbow.builder in phenix with a
smiles string.
You can use something like this to make the cofactor:
http://www.molinspiration.com/cgi-bin/properties
Then use elbow.builder to make the pdb and cif files, and do your
refinements in phenix.
It may be possibl
Hi,
I apologize if this has been posted here before, but I will need to buy a
standard stereo microscope for viewing crystals. Could anyone give me some
suggestions regarding the brand, model, and retailer? Thanks in advance!
Frank
-
Get the
Hello again all,
We have a molybdopterin active site cofactor. It is a
single molybdenum atom, with 2 oxygens and 1 sulfur as
ligands, and coordinated to a pterin ring via 2 more
sulfur atoms. The geometry of the molybdenum is very
roughly square pyramidal.
The issue that we are having involves
Dear All,
We are looking for crystals to test a new device for in situ
changing the humidity
on the X-ray beamline. The requirements are (protein) crystals that are
relatively easy to grow
and that have a clear change in diffraction pattern upon change in
humidity at room temperature.
Any s
Dear all,
we have problems in refining a structure with disorder.
It is a heterodimeric protein and there are only 5 residues
different between the two chains (the structure of the
homodimeric wild type protein is known). The spacegroup is
I4(1)22. It seems that the orientation of the dimers is
s
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