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
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 Nation
Is it a crystal if there are no reflections? Aren't Bragg reflections a
necessary and sufficient condition for calling something a crystal? Ron
On Thu, 30 Nov 2017, Geny wrote:
Dear EveryOne,
I recently tried to collect the diffraction data, but unluckily, the
diffraction patter is atta
I'd like to comment on Kay's statement, "People using a cutoff of 2 (or 3, or 1) for
the mean I/sigI are just using an arbitrary number, as if it were magic."
That may be true for values of 1 or 3, but 45 years ago, I was told by Lyle
Jensen why a 2sigma(I) cutoff was appropriate.
When people
I'm not understanding much of this discussion, but I've noticed the use of
words reminiscent of old issues concerning omega-two theta scans on four-circle
goniostats (see Stout and Jensen, pages 168-173, second edition).
p.s. In my upbringing, crystals were placed on goniometer heads so they c
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. Th
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, you'll
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 yo
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 Ales
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
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:
http://reference.iucr.org/dictionary/
How did people get when using HKL2000? Ron
On Wed, 12 Feb 2014, Phil Evans wrote:
On 12 Feb 2014, at 11:43, Cai Qixu wrote:
Dear all,
Does the I/sigmaI in “Table 1” mean for / or ?
Thanks for your answer.
Best wishes,
Qixu Cai
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 i
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
wrote:
A fascinating discussion (I've learnt a lot!); a quick sanity check, though:
In what scenarios woul
wrote:
I was going to mention that too, 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
wrote:
I'm a little confused. Petsko and others were doing
low-temperature/freezing/vitrification crystal ex
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:
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, Dy
t accepts. That said there is a variation of
> funding that at least our UK agencies will commit to 'Data management
> plans'.
> Greetings,
> John
>
>
>
> 2012/4/5 Ronald E Stenkamp :
>> This discussion has been interesting, and it's provided an intere
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
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 explain
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 distributi
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
"we
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,
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 t
.) wrote:
can anyone point me to a more exact theory of distance accuracy compared
to
optical resolution, preferably one that would apply to microscopy as well.
Stenkamp RE, & Jensen LH (1984) Resolution revisited: limit of detail in
electron density maps. Acta Crystallogr. A40(3), 251
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 believ
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 (or /) to be about as useful as
Rmerge (or its relatives). Ron
On Wed, 9 Jun 2010, James Holton wrote:
Frank von
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, Tab
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 followe
mphasis on crystallographic studies.
Ron Stenkamp
On Sat, 14 Nov 2009, Van Den Berg, Bert wrote:
I wonder, just as a "side note", whether there will still be a (big) need for
X-ray crystallography in a couple of decades?
What will be the state of the art then in structure prediction?
H
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 and
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 the
I've looked at about 10 cases where structures have been refined in lower
symmetry space groups. When you make the NCS operators into crystallographic
operators, you don't change the refinement much, at least in terms of
structural changes. That's the case whether NCS restraints have been appl
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
There are a lot of ways those values can be
affected, in particular in the treatment of the scale factor. And it's been
many years (and many program ago) since the scale factor was under the control
of the user.
Ron Stenkamp
On Fri, 7 Sep 2007, Jacob Keller wrote:
Dear list,
I ha
it's because they
simply haven't found them yet. That statement might be a sign of my
crystallographic arrogance, but it might also be true.
Ron Stenkamp
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