I agree with Frank. This thread has been fascinating and educational. Thanks
to all. Ron
On Sat, 22 Jun 2013, Douglas Theobald wrote:
On Jun 22, 2013, at 6:18 PM, Frank von Delft frank.vonde...@sgc.ox.ac.uk
wrote:
A fascinating discussion (I've learnt a lot!); a quick sanity check,
I've remained silent as this thread evolved into a discussion of how the PDB deals with
water names and numbers. But Nat's comment about the PDB not advertising itself as
anything other than an archival service finally prodded me into saying something.
Something I've slowly come to realize is
How did people get I/sigmI when using HKL2000? Ron
On Wed, 12 Feb 2014, Phil Evans wrote:
I/sigmaI
On 12 Feb 2014, at 11:43, Cai Qixu caiq...@gmail.com wrote:
Dear all,
Does the I/sigmaI in “Table 1” mean for I/sigmaI or I/sigmaI ?
Thanks for your answer.
Best wishes,
Qixu Cai
I agree with George. Sohnke is only six letters and it's been used for a long
time to label these groups. Ron
On Fri, 2 May 2014, George Sheldrick wrote:
In my program documentation I usually call these 65 the Sohnke space groups,
as defined by the IUCr:
Bernhard is giving me too much credit. I just told him I'd seen someone's name
associated with the 65 space groups, but that's the only information I
provided. Ron
On Fri, 2 May 2014, Bernhard Rupp wrote:
Fellows,
my apologies for having sparked that space war.
I wish to interject than in
This discussion has been interesting, and it's provided an interesting forum
for those interested in dealing with fraud in science. I've not contributed
anything to this thread, but the message from Alexander Aleshin prodded me to
say some things that I haven't heard expressed before.
1. The
will commit to 'Data management
plans'.
Greetings,
John
2012/4/5 Ronald E Stenkamp stenk...@u.washington.edu:
This discussion has been interesting, and it's provided an interesting forum
for those interested in dealing with fraud in science. I've not contributed
anything to this thread
There were a number of labs using anomalous dispersion for phasing 40 years
ago. The theory for using it dates from the 60s. And careful experimental
technique allowed the structure solution of several proteins before 1980 using
what would be labeled now as SIRAS. Ron
On Wed, 6 Jun 2012,
I'm a little confused. Petsko and others were doing
low-temperature/freezing/vitrification crystal experiments in the 1970s, right?
(J. Mol. Biol., 96(3) 381, 1975). Is there a big difference between what they
were doing and what's done now.
Ron
On Fri, 16 Nov 2012, Gerard Bricogne wrote:
, but since I was a postdoc of Petsko my words
could have been viewed as biased.
Quyen
On Nov 16, 2012, at 1:26 PM, Ronald E Stenkamp stenk...@u.washington.edu
wrote:
I'm a little confused. Petsko and others were doing
low-temperature/freezing/vitrification crystal experiments in the 1970s
While all of the comments on this situation have been entertaining, I've been
most impressed by comments from Bill Scott, Gerard Bricogne and Kim Hendricks.
I think due process is called for in considering problem structures that may or
may not be fabricated. Public discussion of technical or
Hi.
Perhaps people more familiar with the inner workings of the programs can
comment better on this, but I believe the FOM is simply a measure of how
unimodal and sharp your phase distribution is. If you're working with
experimentally determined phases, you have phase distributions that
Just a few comments on consider a crystal bathed in a uniform
beam.
I've not fully bought into the idea that it's OK to have the
beam smaller than the crystal. I learned most of my crystallography
in a lab dedicated to precise structure determinations, and somewhere
along the line, I picked up
Hi.
Non-crystallographic symmetry (NCS) doesn't apply to the entire crystal, so how
can it give rise to systematic absences? I know it can give rise to
systematically weak classes of reflections, but they aren't entirely absent.
Ron
On Thu, 11 Dec 2008, Winter, G (Graeme) wrote:
One of
Hi.
If the most precise and accurate description of your crystal structure is the
orthorhombic one, you should average the replicated reflections and refine the
structure in C2221. If the crystals are orthorhombic and you refine and report
it in C2, you're producing a model that is larger
But at some point, getting a clear map might not be the goal. If you're in refinement mode, the weak reflections also provide information that your model needs to fit. I find I/sig(I) (or I/sig(I)) to be about as useful as
Rmerge (or its relatives). Ron
On Wed, 9 Jun 2010, James Holton
How you choose to make use of (or ignore) crystallographic symmetry comes down to your
view of what constitutes the best model for the sample you're studying. How
similar do you believe the molecules are in your crystal? If you describe the model in a
higher symmetry space group, you believe
Something related to the results in the 1984 paper, but never published, is
that the calculated electron density for an atom with a B of 100 Angstroms**2
is so flat that you wonder how those atoms can be seen in electron density maps.
Ron
On Thu, 23 Dec 2010, Bernhard Rupp (Hofkristallrat
Maybe counting reflections is dull and boring, but doesn't it make you wonder
sometimes when two programs read the same file and end up with different
reflection counts? What sophisticated mathematics or logical conditions make
it such that progams can't mimic adding machines? What else are
Discussions of I/sigma(I) or less-than cutoffs have been going on for at least
35 years. For example, see Acta Cryst. (1975) B31, 1507-1509. I was taught by
my elders (mainly Lyle Jensen) that less-than cutoffs came into use when
diffractometers replaced film methods for small molecule work,
Could you please expand on your statement that small-molecule data has essentially no weak
spots.? The small molecule data sets I've worked with have had large numbers of unobserved
reflections where I used 2 sigma(I) cutoffs (maybe 15-30% of the reflections). Would you consider those
weak
James, could you please give more information about where and/or how you obtained the
relationship sigma(I)/I = 2*sigma(F)/F? A different equation,
sigma(I)=2*F*sigma(F), can be derived from sigma(I)^2 = (d(I)/dF)^2 * sigma(F)^2. I
understand that that equation is based on normal
James Holton suggested a reason why the forefathers used a 3-sigma cutoff.
I'll give another reason provided to me years ago by one of those guys, Lyle Jensen. In
the 70s we were interested in the effects of data-set thresholds on refinement (Acta
Cryst., B31, 1507-1509 (1975)) so he
The rumblings here at the Univ. of Washington among the computational modelers is that
some of their current models might be more representative of protein structures in
solution than are the crystal structure models. It may take less than a couple of
decades for a reduced emphasis on
I appreciate learning that the R32/H32 tangle was based on a wwPDB
recommendation. For some reason, I find it calming to view this as a PDB issue
and not a ccp4 one. Ron
On Tue, 15 Dec 2009, Eleanor Dodson wrote:
Just a correction - ccp4 had NOTHING to do with H32 definitions - just
Hi.
I'm a little reluctant to get into this discussion, but I'm greatly confused by
it all, and I think much of my confusion comes from trying to understand one of
Ian's assumptions.
Why are the scattering factors viewed as dimensionless quantities? In
the International Tables (for example,
I think the answer is in this paper:
LOW-RESOLUTION ELECTRON-DENSITY AND ANOMALOUS-SCATTERING-DENSITY MAPS OF CHROMATIUM HIGH-POTENTIAL IRON PROTEIN
By: STRAHS, G; KRAUT, J
JOURNAL OF MOLECULAR BIOLOGY Volume: 35 Issue: 3 Pages: 503- Published:
1968
On Fri, 29 Aug 2014, Alexander
Watch out with oils and oxygen. Oxygen is fairly soluble in oils. When we
worked on deoxyhemerythrin, we had to degas our sealing wax to keep things
anaerobic. If you heat wax, and then put it in a vacuum, it'll froth as all
the gases come out of the liguid. Then of course it hardens and
Are most stereo images now for cross-eyed viewing? I thought they were for
wall-eyed viewing.
Perhaps a warning would be helpful for people starting out at looking at
published stereoviews. If you look at a stereoview constructed for wall-eyed
viewing but look at it with crossed eyes,
I also wondered about the statement about oils blocking diffusion of O2. We
had lots of trouble keeping things anaerobic in a glove box until we degassed
the oils and waxes used to mount crystals in capillaries. We found that
putting them under vacuum removed much of the dissolved oxygen.
I don’t know about the myth thing, but I remember Martha Teeter describing
pentagons of waters in crambin.
Here’s a reference:
Water Structure of a Hydrophobic Protein at Atomic Resolution: Pentagon Rings
of WaterMolecules in Crystals of Crambin M. M. Teeter Proceedings of
the
K2HgI4 worked for solving hemerythrin in 1975. The various species of HgIx in
the solution found several binding sites. Some were single Hg atoms between
cysteines and others were HgI bound elsewhere. Ron Stenkamp
From: CCP4 bulletin board on behalf of
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