Hello all,
Does anyone have a rough estimate (or has anyone actually determined) an
average dead/delay volume between buffers run on an AKTA Prime FPLC? We are
attempting to overexpress/isolate a smaller His-tagged transmembrane protein,
and require running several detergent buffers in success
(this seems not the case)
> c) too many overlaps during collection, mosaicity
> Guess 1) is your case, if I can.
>
> Also, good R factors from low-completeness (either reason
> above) is
> less reliable.
>
> Good luck.
>
> Lijun
>
>
> On Aug 20
t; Subject: Re: [ccp4bb] Lower completeness, decent R factors, but low B
> factor...
> To: CCP4BB@JISCMAIL.AC.UK
> Date: Wednesday, August 20, 2008, 4:30 AM
> James Pauff wrote:
> > Hello all,
> >
> > I have a refined structure at 2.6 angstroms that at
> about 73% comp
To: [EMAIL PROTECTED]
> Cc: CCP4BB@jiscmail.ac.uk
> Date: Wednesday, August 20, 2008, 4:30 AM
> James Pauff wrote:
> > Hello all,
> >
> > I have a refined structure at 2.6 angstroms that at
> about 73% completeness at this resolution. The I/sigma is
> about 2.0 at 2.6 ang
Hello all,
I have a refined structure at 2.6 angstroms that at about 73% completeness at
this resolution. The I/sigma is about 2.0 at 2.6 angstroms, and the omit
density for my ligands is great contoured at 3.0sigma. My Rcryst is 19 or so
and the Rfree is 24.5 or so.
HOWEVER, my mean B value
Hello all,
Silly question, but what is the most convenient means
to find the overall I/sigma and the I/sigma for the
highest resolution shell in CCP4? At the end of
refinement and validation, and after running PROCHECK,
I am still using a very convoluted route to obtaining
these numbers.
Thanks!
Perhaps a silly question, but I've asked at least a
couple of those before...
We have been running CCP4 6.0.2 on Windows and
Macintosh systems, but have recently purchased two
supercomputers that are set up with Linux Fedora 7 for
computational work. We are trying to put CCP4 onto
these computers
Good morning/afternoon, evening again all,
As sort of a "last question" on this current project,
I have noticed that my final input PDB gets altered by
REFMAC when it constructs the output PDB. In the
output _refmac1.pdb file, all of my HETATM records are
changed back to ATOM records, and my TER
Good morning/day/evening all,
I have a structure that is refined, with the exception
of the molybdenum (MoOOS) cofactors (there are two of
them), which are square pyramidal and coordinated to 2
sulfurs in an enedithiolate of a pterin ring. I have
brought up my issues with refining this before in
Shivesh,
Having gone down the "needles vs. crystals" route
recently, my two suggestions would be:
1) Lower the protein concentration to 10 mg/ml
2) Slightly lower your precipitant percentage, say to
26%. My situation involved PEG4000, and I noticed
that modifying the protocol to PEG8000 at a sl
Good day all,
I have a metal center in my enzyme active site, in a
roughly square pyramidal coordination. I know from
EXAFS and other work how this coordination sphere
should look, but following REFMAC the cofactor here
does not end up realistically coordinated/oriented.
Although it is in the de
Hello again all, sorry to clutter your inboxes...
With regards to my problem of connecting a
Molybdopterin correctly, does anyone have suggestions
as to the use of LINK statements in my coordinate
file? Or the use of LINK statements at all? This was
an idea when we first started refining the str
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
Good day all,
What is the best means of getting a freeR column into
an existing mtz file? I've noticed the "Edit MTZ"
command bar in CCP4, but there are other options (such
as conversion to XPLOR and then back to MTZ) that seem
to be able to accomplish the same thing, although
there appear to be
ing" amino acid that has
the occassional visible R group.
Just wondering what this means, that I am seeing
stellate points that seem to be acting as place
holders for my residues in a couple locations in my
structure. The structure was obtained using molrep.
Th
Thank you all, that was much easier than I expected.
Best,
Jim
Boardwalk
for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's
economy) at Yahoo! Games.
http://get.games.yahoo.com/
Good day all,
First off, thank you all so much for your help a
couple days ago! I just have a quick question
regarding the use of CCP4 to generate density maps.
Is there a way to generate a map(s) that can be read
into PyMol? I understand that PyMol can only read CNS
or XPLOR maps, is this corr
> using the difference
> > density map at this point. Then go to
> Calculate/Merge Molecules and
> > select which one you want to merge, save the new
> coordinates including
> > your found ligand.
> >
> > Good luck,
> >
> > Juergen
&
Good day all,
I have what may be a very simple question. I am
trying to insert a substrate/ligand into the active
site of my enzyme using COOT, into electron density
that I have already utilized in "O" for this purpose.
I've created the substrate library file (*.cif) using
a pdb file from PRODRG
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