It totally depends on what you define as your C-H bond length.
For XRD work, the C-H is the distance between the electron
center-of-masses. For neutron or high-resolution XRD work, you can
determine the distance between the nuclear center-of-masses. They are
different by about 0.1A. The electro
Can someone point me to bulletpoint documentation on using the twin
refinement in CCP4?
Here's what I did.
1. I'm in space group P3, and the see a very clean diffraction pattern
that looks like one single lattice. Very clean spots, so merohedral
twinning.
2. You can use various programs to est
I appreciate all of the comments and suggestions on how to locate a better
CIF file for ATP. I adopted the suggestion of Boaz, and generated a new
ATP.cif file, and refined one of my structures.
The validation server still uses substantially different target bond
lengths and angles, so there is be
Divide by 11 if you count all atoms, including H-atoms; divide by 20-22 if
you only count non-H-atoms, to get the approximately number of atoms in
the unit cell.
On Mon, May 5, 2014 6:07 am, Natalie Tatum wrote:
> Hi all,
>
> I've had an interesting question from an undergradute student, asking i
Is there a reason why you must use restraints with metal coordination?
The main reasons that you use restraints in protein refinement is to
reduce the number of free variables in the refinement, and because the
"resolution" isn't sufficient to resolve two atoms separated by the
typical carbon-carb
The new CCP4I interface for PHASER removed the menu item where you could
change the number of clashes. It's not set as a default to 5% of the
number of C-alpha atoms. Where is the default file?
I found the phaser_MR.def file in share/ccp4i/tasks, and changed the
parameter value, but it still used
No, I listed a few recent ones
V. Gaur, et al., Plant Physiol., 152(4), 1842-1850 (2010)
O. Antipova, J Biol Chem. 2010 Mar 5;285(10):7087-96. Epub 2010 Jan 6.
Y. Nakajima, J Bacteriol. 2008 Dec;190(23):7819-29. Epub 2008 Sep 26.
S. Stayrook, Nature. 2008 Apr 24;452(7190):1022-5.
Many MIRAS,
Remember that it's all relative to the length of the FP vector. If your FP
vector is small, then the f" component can substantially change the phase,
even with a small f" component. So if you have measured a number of
relatively weak reflections with minimal error, there is a substantial
anomalous
Most beamlines have attenuators, so there's little reason to collect
multiple sweeps. We always collect 360deg. Since it's a small molecule,
and usually fairly large and robust, you can warm it up, nudge it in a
different direction with a pin (we use sterile, disposable acupunture
needle), and refr
I just installed CCP4-6.2.0 and COOT on a Red Hat v6.1, x86, linux
workstation. Some of the menus, along the right edge, are gray buttons on
gray background. Where is the preferences file to change the colors of the
menu buttons? The menus across the top of the window are fine.
Also, idiffdisp is
I've had problems too. Some of the files are non-readable, so you need to
do a
sudo chmod -R a+r *
to make them readable. Also it looks like the libraries changed a bit (at
least for ADP).
Bernie
On Fri, July 29, 2011 2:08 pm, Yuri wrote:
> Dear all,
> I have just downloaded and installed the c
That's a really old paper. You can purchase the lysozyme from Hampton
Research and it's fine. The recipe is available from the Hampton Research
page:
http://hamptonresearch.com/product_detail.aspx?cid=28&sid=173&pid=524
Grow them a low temp and you can stop them when they are the right size.
I f
Dear Ian,
Well, "it" *IS* broke. If you are running some type of process, as you
implied in referring to LIMS, then there is a step in which you move from
the crystal system and point group to the actual space group. So, at that
point you identify P22121. The next clear step, automatically by soft
Ian,
I think it's amazing that we can program computers to resolve a < b < c
but it would be "a major undertaking" to store the matrix transformations
for 22121 to 21212 and reindex a cell to a standard setting. I was also
told that I was lazy to not reindex to the standard setting when I was a
gr
Interesting. My IT, both volume I and volume A (1983) only have P21212 for
space group #18. Do I have to purchase a new volume A every year to keep
up with the new conventions?
Cheers,
Bernie
On Thu, March 31, 2011 12:57 pm, Ian Tickle wrote:
>> I would like to share my experiencde with a rathe
If you are using CCP4, it can accomodate P22121. However, just reindex in
CCP4 to the correct setting with P21212.
Bernie Santarsiero
On Thu, March 31, 2011 9:28 am, Anita Lewit-Bentley wrote:
> Dear all,
>
> I would like to share my experiencde with a rather unexpected problem
> of indexing con
This was mentioned in Marv Hackert's outgoing remarks at the ACA meeting a
few years ago, and he showed the clip of the scene. Jimmy Stewart's
comment is apt: "It's quite fundamental. It's really odd to me that the
schools don't teach it."
Bernie
On Sun, March 27, 2011 4:13 pm, harry powell wrot
Ditto. YES, still generally prefer CNS v1.3 to REFMAC, especially due to
composite and simulated-annealing maps.
Different set of flagged reflections, so it might very well be different.
Also, the low-resolution solvent scaling is different between the two
refinements.
Bernie Santarsiero
On W
I think you should just grab a copy of Stout and Jensen, and use the
oscillation photographs directly. What's so special about a precession
image? You can still index the spots and follow along rl lines.
Bernie Santarsiero
On Thu, June 25, 2009 1:38 pm, Francis E Reyes wrote:
> Yes this is exac
The other approach is to choose a reasonable B-factor from the atoms and
ligands in the vicinity, fix the B's, and then refine the occupancy.
It is true that the occupancy and B-factor of an atom are highly
correlated with full-matrix least-squares refinement. The only
discrimination comes from hi
Empirically, you can leave out a couple of "average" atoms in the
structure, and recalculate the maps. If you leave out a O, N, and C atom,
with relatively average B's, then you know how many electrons you should
be seeing for each in the difference map. Note that the peak height will
vary due to e
We were on a Br-soak flurry for awhile, and when I also talked to others,
it would work about 20-30% of the time. A few years I compared a structure
with Se-Met and native with Br-soak. There were four Br's at about 30%
occupancy, and it phased fine. It wasn't as good as the Se-Met phasing,
but we
We've been able to run months with an old Xstream 2000 system, so that
shouldn't be the problem. Unlike Frank, we haven't had problems with water
in the nitrogen from a nitrogen generator.
If Frank is correct, that it's water, then either the molecular sieves
need to be replaced, or there is ice b
In parallel with the discussion around this off-CCP4-topic, are they any
good examples of the opposite case, where the protein is a monomer in
solution (as evident from light scattering, MW determination through
centrifugation, EPR, etc.) but crystallizes as a dimer or higher multimer?
Bernie Sant
PDBSum is the easiest to use for this, and some other useful information:
http://www.ebi.ac.uk/pdbsum/
Bernie
On Mon, November 10, 2008 12:34 pm, hari jayaram wrote:
> Hi CharuEspript is an excellent resource for this
> It is particulary useful when you want a secondary structure schematic
> wit
My use goes back to Evans and Sutherland workstations, FRODO, SGI's with
O, Duncan's graphics program suite, and COOT, on multiple platforms.
I don't use dials at all, and multiple uses with a three-button mouse are
far more favorable.
I still prefer O to COOT for a number of reasons. The main re
Friedel pair is strictly F(hkl) and F(-h,-k,-l).
Bijvoet pair is F(h) and any mate that is symmetry-related to F(-h), e.g.,
F(hkl) and F(-h,k,-l) in monoclinic.
There are always anomalous differences, though they can be unmeasurably
small.
Bernie Santarsiero
On Thu, June 26, 2008 10:55 am, Bernh
Bernhard,
It's complicated. The last two columns are related to atomic Z number and
group occupancy. They used a different equation than the typical
Debye-Waller equation to calculate a sort of B-factor and get the electron
density maps.
Bernie Santarsiero
On Fri, June 20, 2008 4:05 pm, Bernhar
Dick Dickerson tried to do the same thing at Caltech around the same time.
The major problem with cooling equipment was that the Picker goniometer
had lots of metal in it, and each of the metal pieces cooled and
contracted differently, so the alignment was always off. Nice idea, but
not useful. Tha
I typically collect data at -50C on all small molecule samples. I've had
quite a few cases where there are phase transitions, and you can damage
the crystals, especially when the molecules are packed in a pi-pi stacking
motif, or I'm dealing with alloy systems.
I've also collected data at 16K, so
Depending on your time, I'd recommend adding the use of a native gel band
shift to try a one that doesn't work and one that does.
http://www.doe-mbi.ucla.edu/~sawaya/m230d/Crystallization/crystallization.html
I know you can use NaBr or NaI to grow lysozyme crystals as well, and they
stick on hydr
On Fri, March 28, 2008 10:13 am, Lucas Bleicher wrote:
> Some time ago I've heard about the idea of proposing
> an ensemble of models (as in NMR), instead of a single
> model for x-ray crystallography structures. If I
> remember correctly, this idea has been published
> somewhere. Can anyone tell m
I use XDSCONV to make the mtz file using all of the reflections. Then I
use uniqueify in CCP4 to make sure the asymmetric unit is correct for
CCP4, and tag the test set.
Bernie Santarsiero
On Thu, February 21, 2008 9:32 am, Dirk Kostrewa wrote:
> Usually, I run CAD first after F2MTZ to make sure
The only other comment that I'd add is XDS builds real three-dimensional
profiles, whereas HKL2000 uses two-dimensional profiles. Thus, you can
imagine that if you have already defined a 3D profile, XDS only needs part
of the reflection, over one or more images, to estimate the overall
intensity of
in a
> paper which would report chi-suqares.
>
> I am afraid I may be misinterpreting what you were trying to say - I
> apologize if that is the case.
>
> Cheers,
>
> Ed.
>
> Santarsiero, Bernard D. wrote:
>> You know there is that other funny column with chi^2&#
You know there is that other funny column with chi^2's. I like to quote
both. Half of the reviewers will know which column to look at, but you
will satisfy the other half.
Bernie
On Fri, January 18, 2008 1:39 pm, Edwin Pozharski wrote:
> There are two opposing views on this.
>
> First: Rmerge do
I seem to recall hearing Rsym first when I used the Xuong-Hamlin detector,
since there were a substantial number of redundancies. There were two
Rsyms, one called Rrms for the sqrt over the sum of weighted squared
differences and and Rav for the linear summation of unweighted
differences. This was
In our original work on a prototype, we used the Cartesian technology. We
were able to dispense 10nL+10nL drops with a large range of viscosities
without difficulty. The main issue was to wash the tips after use to
prevent clogging. That was with a system that could dispense 1nL droplets.
The prese
I would also ask what is the actual goal in refining the occupancy of the
ligand?
While I agree wholeheartedly with George, the B-factors will adequately
model a lower ligand occupancy. Usually the question you want to resolve
is "Is the ligand really bound in the active site, or is this an artif
The main reason was related to absorption. If you didn't completely bathe
the crystal in the xray beam, then the diffracting volume of the crystal
would be different during the data collection, and thus, scaling would be
inaccurate, especially when there was radiation damage. This was
especially tr
One of the major problems with any R-factor is that it's a function of the
denominator, and therefore I, F^2, or F. Depending on how you "push" to
higher resolution, the R's will very likely increase due to the dominance
of the denominator over the numerator. It's good to also monitor on
evaluation
On Wed, October 10, 2007 11:50 am, Bryan W. Lepore wrote:
> On Wed, 10 Oct 2007, Jim Pflugrath wrote:
>> It has come to my attention that the wavelength of a Copper Kalpha may
>> have changed over the years. At least this appears to be true if you
>> look at the International Tables.
>
> the 'natu
My usual targets are 0.010 for the bonds and 1.50 for the angles.
Bernie Santarsiero
On Tue, September 11, 2007 3:22 pm, Lari Lehtio wrote:
> Hello!
>
> Jaskolski & other experts say in "Stereochemical restraints revisited: how
> accurate are
> refinement targets and
> how much should protein st
On Fri, August 17, 2007 10:56 am, Eleanor Dodson wrote:
> There are obvious ones like - incomplete structure etc, but have you
> tried TLS? Sometimes this can dramaticaly improve the R factors.
>
When people run TLS, are they trying to improve the R-factors, or actually
generate a reasonable mo
Sorry, I think it's a waste of resources to store the raw images. I think
we should trust people to be able to at least process their own data set.
Besides, you would need to include beamline parameters, beam position,
detector distances, etc. that may or may not be correct in the image
headers. I'
Can I ask a dumb question? Just curious...
Why are we now limited to 80 "columns"? In the old days, that was a limit
with Fortran and punched cards. Can a "record" (whatever it's called now)
be as long as we wish? Instead of compressing a lot on a PDB record line,
can we lengthen it to 130 columns
I agree with Kevin. We have stereo on about half of our workstations, and
no one has used them in about three years. We typically use "O".
Also, we have three large servers which are relatively fast. So the main
purpose of a workstation is building, not computing here. That way you can
easily work
I seem to recall this being discussed at some point.
For the difference electron density map, there clearly isn't a downside to
loss of reflections, i.e., the coefficients in the map generation are
formally zero for Fo-Fc (which all the scaling, weight, sigma-A bits in
there). If the phases are fa
On Thu, March 22, 2007 3:46 pm, William Scott wrote:
> Hi Citizens:
>
> Does anyone use an uninterruptible power supply for their X-ray
> generator? Here at UCDIY, the electricity supply is pretty sketchy,
> and it is hammering our X-ray generator every time someone forgets to
> feed the hamster o
My guess is that the integration is roughly the same, unless the profiles
are really poorly defined, but that the scaling that is suffering from
using a lot of high-resolution weak data. We've integrated data to say
I/sig = 0.5, and sometimes seem more problems with scaling. I then cut
back to I/si
There are journals that have specific specifications for these parameters,
so it matters where you publish. I've seen restrictions that the highest
resolution shell has to have I/sig > 2 and completeness > 90%. Your
mileage may vary.
I typically process my data to a maximum I/sig near 1, and compl
It would be useful to know how you tried to solve the structure by MR.
Just because there is a large number of chains in the ASU isn't a reason
that MR will fail. At times you need to find some of the chains, do some
rebuilding, and then use that amended model for a continued search.
Bernie Santar
I'm sure that the relative weight between your structure factors and
geometric factors is wrong. If you use the default value, 0.3, it may or
may not be too high. In CNS, the relative weight factor is calculated, but
this is not done in REFMAC. As a rough rule-of-thumb, I aim for a rmsd of
bond len
ile?
>
> I dont think you need to do this..
> Eleanor
>
> Santarsiero, Bernard D. wrote:
>> Not purely a ccp4 question, but an MTZ file is involved, so stick with
>> me.
>>
>> I've collected a SAD data set, and processed with XDS. I can use XDSCONV
>> to
Not purely a ccp4 question, but an MTZ file is involved, so stick with me.
I've collected a SAD data set, and processed with XDS. I can use XDSCONV
to generate an MTZ, SHELX, and CNS file. I chose the MTZ file since it
keeps the intensities. SHELX does too (the F**2), but has separate lines
for (h
On Mon, March 5, 2007 2:16 pm, Nat Echols wrote:
> I had a debate with a coworker about using MR in desperation and I'm
> curious what the most extreme case is where a very different model was
> used to solve a structure. This could be highest RMSD, lowest % identity,
> or most incomplete model.
-
It's very possible with any overlap of lattice points, even in the lower
symmetry space groups. To extend Eleanor's list: For example, I once had a
structure with the unit cell relationship 3c cos(beta) = -a. In cases like
that, it's not really a c
It's very possible with any overlap of lattice points, even in the lower
symmetry space groups. To extend Eleanor's list: For example, I once had a
structure with the unit cell relationship 3c cos(beta) = -a. In cases like
that, it's not really a clean diffraction, but looks very much like a
single
You didn't say anything about the "weighting term" between the F's and
geometrical parameters. That will substantially affect the R's, and the
default value of 0.3 in REFMAC isn't appropriate for all structures. In
CNS, it's adjusted to a more reasonable value during refinement.
Bernie Santarsiero
Assuming that the MR solution is correct (I agree with Eleanor, that you
need to be certain about your selection of space group), then use your
complete model of chain A superimposed on chains B, C, and D. Then refine
and build the heck out of it. In a similar situation, it was relatively
easy for
t;Fifty Years" of a "B factor"
>> but it sounds as though Waller decided to use a different
>> nomenclature in his paper from 1927 to avoid confusion.
>>
>> Too bad that "Fifty Years" is no longer in print, though used copies
>> can be purchased
It looks like the earliest reference to the Debye-Waller factor is from
Debye's paper:
Uber den Einfluss der Warmebewegung uf die Interferenzerscheinungen beiu
Rontgenstrahlen, Verhandl. deut. phyik. Ges., 15, 678-689 (1913),
and the succeeding paper Verhandl. deut. phyik, Ges., 15, 738-752 (1913
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