Dear ALL:
Sorry for this kind of off-topic question.
I am going to co-crystallize one protein with cholesterol. I read some
papers saying that
their protein can be pre-incubated with 1mM cholesterol in the presence of 5%
(v/v) ethanol.
TO do so, I first dissolved cholesterol in 10
Dear Cheng,
You could take your non-diffracting needle urchins and crush them in their
growth solution (vortex several minutes and/or try Hampton seed bead). Then
make serial dilutions of the seed solution and add them to a whole new
screen (the MMS method) or try the optimization method with new
Mariah,
Although your data may be perfectly twinned, more likely your data
'shows about 50 % twinning' because you are not in the correct space
group. How are you determining your twin fraction and in what space group?
Jon
--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Buil
"The problem of discrete values in restraints can be circumvented by
computing
a corresponding continuous value such as a chiral volume Vc, which is given
by
a scalar triple vector product A (B x C) originating at the central atom.
With the
smallest ligand pointed toward the observer and clockwis
Sorry, the original post looks garbled (mirroring my internal state,
no doubt). I'm trying again, sending as plain text:
Friends,
A question about the definition of chiral volumes:
I'm looking for the definition of the SIGN of a chiral volume. The
only ccp4 reference I can find (readily) i
Friends,
A question about the definition of chiral volumes:
I'm looking for the definition of the SIGN of a chiral volume. The
only ccp4 reference I can find (readily) is this:
http://www.ysbl.york.ac.uk/~garib/refmac/docs/theory/chiral.html
This page gives an algorithm for determini
Move the beam stop back? My lab has grown quite a few
crystals that only diffract to very low resolution.
Phoebe (with sympathy!)
Original message
>Date: Mon, 19 Apr 2010 11:35:11 +0800
>From: tat cheung cheng
>Subject: [ccp4bb] Re： [ccp4bb] Mysterious Crystals?
>To: CCP4BB@JIS
Hi Pavel
AFAIK it's not in the literature, in fact I wasn't even aware it was
in phenix, but that's probably only because we don't use phenix
(sorry! - being commercial we would have to pay for it!). The problem
is always where you put little tidbits like this, unless it's part of
a much bigger p
Hi Ian,
... or you could just use the RMSD of the difference map (i.e. that
using 2(mFo-DFc) coefficients for acentric reflns), which is a
reasonable approximation of the uncertainty provided most of the
structure is accounted for, as the uncertainty of the Fourier map
(i.e. that using 2mFo-DFc
Hello:
some more on water picking...
After quite a bit of experimenting, I found this working the way I like
(implemented in phenix.refine):
1) peak at mFo-DFc map is higher than ~3sigma, and
2) peak center is within a hydrogen bond to another atom (water or
macromolecule), and
3) peak has a
... or you could just use the RMSD of the difference map (i.e. that
using 2(mFo-DFc) coefficients for acentric reflns), which is a
reasonable approximation of the uncertainty provided most of the
structure is accounted for, as the uncertainty of the Fourier map
(i.e. that using 2mFo-DFc for acentri
The newest refmac will deal with this and generate maps with twinning
corrected..
Eleanor
protein.chemist protein.chemist wrote:
Hi All,
I have a dataset that shows about 50 % twinning. I was curious what will be
the best way for the refinement and calculation of electron density maps,
includ
Has anybody ever explored contouring maps using a "sigma" (i.e. rmsd)
derived only from what is clearly the solvent region?
Obviously that's not relevant during early phasing, but in the later
stages of refinement, that would be relatively clear. And it would be
fairly comparable from map to
Jim Pflugrath calls it "molecular substitution" -- I find this a very
neat distinction.
On 19/04/2010 15:50, Ian Tickle wrote:
I would say it should still be classed as MR: the distinguishing
feature of MR is surely that it uses an known structure as a starting
model, not that it does a rotati
Hello -
The sigma issue a bit more complicated.
What we call usually sigma is the root mean square deviation (rmsd) of
the map.
Lets first recall, that the variation within the protein region is
quite large, while the solvent is rather flat.
Now, lets take an 'extreme' example, of a prot
Hi All,
I have a dataset that shows about 50 % twinning. I was curious what will be
the best way for the refinement and calculation of electron density maps,
including the composite omit map.
Thanks a lot.
Mariah
--
Mariah Jones
Department of Biochemistry
University of Florida
Couldn't they simply be too thin? After all, unit cell dimensions are
routinely about 0.01um, so if these needles are only fraction of a
micron thick, there is simply not enough material for diffraction.
Nice looking but non-diffracting protein crystals are too disordered
(i.e. while packing is p
I would say it should still be classed as MR: the distinguishing
feature of MR is surely that it uses an known structure as a starting
model, not that it does a rotation/translation search. In any case
the distinction between a rigid-body search and RB refinement is moot.
At Astex our automated s
I second Tim's opinion. In the days of CNS/O, there was a popular rule
to place waters in 3 sigma peaks that make chemical sense, then
re-refine and keep those waters that produce more than 1 sigma in 2fo-fc
map. (With Coot the default cutoff is 5).
There could be a bizarre probabilistic argumen
Well, the good news is that they don't seem to be "salt" crystals. But have you
really ruled that out? With small molecule crystals the diffraction pattern is
so sparse, and at such high resolution, that you are likely to miss it
altogether
in a one-degree oscillation and looking for spots around
Quite a lot of structures in the PDB involve minor variations on structures
that have already been solved (different ligands, mutants, high res), so the
"solution" involves refining the previous structure against the new data,
perhaps starting with rigid body refinement to correct minor variations
I would like to extend this to Pittsburgh as well. We are in Eastern
Pittsburgh, available by bus or taxi to Pittsburgh International Airport. We
have wireless internet but not much apartment space. If you are stuck in
Pittsburgh, please send me an email to make arrangements.
Regina
-
Jürgen,
PyMOL sessions are essentially pickled Python dictionaries. At this
point I'm not aware of a way to easily merge the contents of two
sessions. This would be a nice new feature; I've added it to my list
of features enhancement requests.
Thanks,
-- Jason
On Sun, Apr 18, 2010 at 6:36 PM,
Dear depositors,
does exist there any program that is able to handle the beta-sheets of
complicated structures
like beta-helices, bifurcated sheets ... to produce the input for
PDB-deposition. The program included in
the PDB-deposition procedure failes in our case and there are lots of strands
a
Any applicants for this Summer School who have not already done so should
pre-register by 1st May 2010, on which date the WWW site will close.
As stated on the pre-registration form, applicants will not be
considered for a place on the School unless a supporting letter from their
supervisor has
Perhaps this is a case of a 'phantom crystal' that was discussed on the CCP4bb
awhile back:
http://bit.ly/b6Rgw7
All the Best,
Sean
Here are my "counts" of the various methods used for PDBs as of a few
days ago:
37851 MR
7802 MAD/SAD
NULL
669 OTHER
53 N/A
993 MIR
352 SIRAS
316 MIRAS
188 AB-INITIO
88 SIR
6 RIP
2 UNCONVENTIONAL
1 UNCONVENTIANAL
1 FIBER-DIFFRACTION
56171 TOTAL
The other 8605 don't have REM200 entries.
N
Thanks to several people for helpful comments to my question on the Proportion
of MR in the PDB.
I got two very detailed responses one from the OCA team at the Weizmann which
went to the Bulletin Board
"This is what OCA has: From un total of 64,623 PDB structure files,
30,784 have 'MOLECULAR R
Wasnt it the tramp whom they beat to death - and the book was R James..
That movie gave the cold shivers..
eleanor
Philip Leonard wrote:
I have a vague recollection of a student carrying books about
crystallography getting beaten up at the start of Clockwork Orange. This
might only be in the b
Hi all -
I must say that I do agree with Tim. Either Refmac/Coot or Refmac/
ARP_waters do a good job (so does other software) but I always check
things manually.
The most obvious problems with software are:
-Putting waters in place of ions - when you think of chemistry you
will realize tha
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