Some details of one controversy Prof. Rich became embroiled in are available
on the wikipedia page for his colleague Sung-Hou Kim
(http://en.wikipedia.org/wiki/Kim_Sung-Hou).
Especially references 6-8, which are scanned copies of correspondence exchanged
with the folks at MRC, e.g. the initial
Also collect while rotating around the long axis, which you nearly are in this
shot assuming the Phi axis is horizontal.
That way the close separation is in x,y where you can see it rather than in Z
which puts the spots on top of each other requiring thin slicing and (low
mosaicity!) to
On 04/20/2015 06:44 PM, xaravich ivan wrote:
Hi CCP4eans,
solvent based HPLC system?
Do you mean like acetonitrile:water:TFA on reverse-phase columns? I think this
is
routinely used for analytical runs or to obtain material for protein chemistry,
but the concentration of acetonitrile
One of my projects was caught in the transition- as long as we didn't have
crystals diffracting to high resolution, the project was highly significant
but was denied (continuation of) funding for lack of confidence we
would get the structure. After we got good crystals and phased them
they said
On 04/01/2015 08:47 PM, Shane Caldwell wrote:
I guess the next, probably more general question for the bb is: which utilities
export an NCS transformation matrix with more precision?
TAJones' O program allows you to specify output format like
write .LSQ_RT_m2m ncs.odb (3f16.10)
which gives
To be sure it is protein, it would be nice to see some spots at resolution less
than (spacing greater than) ~12 A. The pattern is somewhat consistent with a
unit cell with two very short axes and one long axis. If so, then when you
rotate so that the long axis is in the plane of the picture
Do you have evidence that the oil blocks diffusion of O2? O2 is a nonpolar
molecule, generally much more soluble in oils than in water. I'm not sure about
silicone oils, but I would think they also dissolve O2 readily.
eab
On 03/18/2015 08:02 AM, Patrick Shaw Stewart wrote:
Hi Steve
I have
Actually I may have misunderstood the original post. Patrick never said oils
block O2 diffusion:
On 03/18/2015 09:47 AM, Edward A. Berry wrote:
The microbatch-under-oil method is very handy for anaerobic work:
(In a glove box, of course)
1. You can keep the microbatch
If you use restraints to fix outliers, I strongly suggest to refine to convergence without
restraints after they are fixed. If some outliers return, and % favored
decreases, so be it.
For one thing, depositing a structure with dihedrals restrained gives an unfair
impression of higher quality
: Edward
Ethanol? You weren't setting up drops with liquor on your breath, were you?
On 02/23/2015 12:20 PM, Keller, Jacob wrote:
Dear Crystallographers,
I've got a strange blob hanging off an arginine--see attached. Any ideas?
Nothing weird in the prep; cryst+prot conditions: NH4SO4, TRIS/HEPES,
Well let me further muddy the waters by insisting that the 1 IS DEFINITELY a
place-holder, telling you that there is no rotation (greater than 1-fold) along
the a or b axes, and that the 2 therefore refers to 2-fold rotation along the
next axis, the ab diagonal (no the -a,b diagonal which is
However it is important to note that there are real non-proline cis peptides in
high-resolution structures, and to not throw out these babies with the
bathwater! In fact I think they are probably under-represented because people
are hesitant to build a non-pro cis peptide even when the
, A., and Wampler, J. E. (1990) J. Mol. Biol. 214, 253–260
D. Pal, P. Chakrabarti, Cis peptide bonds in proteins: residues involved, their
conformations, interactions and locations, J. Mol. Biol. 294 (1999) 271–288.
(and I'm sure that is far from complete)
On 02/16/2015 12:30 PM, Edward
Is the old mosflm.lp open in an editor?
Some editors will put a lock on the file which would prevent mosflm from
overwriting or renaming it.
On 02/03/2015 11:38 PM, Keller, Jacob wrote:
Dear Crystallographers,
Has anyone come across this message before with imosflm in Win7? I think
Include the ligand residue in the NCS restraint-group to which the surrounding
protein residues belong?
On 01/30/2015 08:24 PM, Ethan A Merritt wrote:
On Saturday, 31 January, 2015 00:51:08 Jurgen Bosch wrote:
Hi Ethan,
DM with a mask of the ligand in chain A then applying the NCS
Also RAID (REDUNDANT array of inexpensive disks). To me redundancy implies
robustness, overdetermination, like when I measure absorbance at 1500
wavelengths to calculate the concentration of five absorbing species with a
2-parameter baseline offset.
Exactly the connotation we want for our
convergence, no matter how many cycles of refinement you run.
eab
Best,
Tim
On 11/25/2014 07:29 PM, Edward A. Berry wrote:
provided the jiggling keeps the structure inside the convergence
radius of refinement, then by definition the refinement will produce
the same result irrespective
will). I agree that an RMSD of 0.054 should be well within the radius of
convergence at 1.8 A.
Cheers
-- Ian
On 4 January 2015 at 17:50, Edward A. Berry ber...@upstate.edu
mailto:ber...@upstate.edu wrote:
On 11/25/2014 01:41 PM, Tim Gruene wrote:
Hi Ed,
it is an easy
range), then by getting outside of that zone but still
within radius of convergence, I might have seen it return to a point
satisfactorily
close to the starting point. Case not closed yet!
On 01/04/2015 06:21 PM, Edward A. Berry wrote:
I didn't think about that. Yes, weights were being re
bacterioferritin in the I422 space group, like 1JGC, has a trimer in the
asymmetric unit, but the biological unit is 24-mer! Looking at it another way,
considering a dimer is two monomers crosslinked by a heme, the asu contains 1.5
dimers and hence 1.5 hemes!
eab
On 12/11/2014 07:27 AM, Hay
Your .eff file must be explicitly referencing the Ca that you removed. Since it
doesn't
exist, phenix stops. Search your .eff file for the string
name CA and chain A and resname CA and resseq 1
(maybe a geometry.edit) and remove the reference.
I think the CCP4 bylines specifically encourage
If it is a heme or ironsulfur cluster then the reduced and oxidized forms have
distinctly different spectra. Take a spectrum of your protein reduced with a
few grains of dithionite and oxidized with a trace of hydrogen peroxide or
ferricyanide (take another spectrum of ferricyanide alone since
provided the jiggling keeps the structure inside the convergence radius of
refinement, then by definition the refinement will produce the same result
irrespective of the starting point (i.e. jiggled or not). If the jiggling
takes the structure outside the radius of convergence then the
Using a percentage might be justified as a trade-off between having ample free
reflections for statistics and cutting too deeply into your completeness of
working reflections for refinement.
It seems to be generally agreed that 2000 free reflections is sufficient to
guide your choice of
That is a different question- I thought you already knew which atoms are
duplicates.
To identify them, there are programs that will print a list of pairs of atoms
within
a threshold distance from each other.
But in this case I think plain old sort program will be easiest.
1. Get all the waters
(for developers or whoever manages the .cif libraries. Is there a separate
list?)
PEE has been used (mainly by me) for the natural lipid PE
(1,2-Distearoyl-sn-glycero-3-phosphoethanolamine),
but the current PEE.cif specifies the wrong chirality about the glycerol C2
atom,
giving un-natural
For even smaller volumes, make a dialysis button from an eppendorf tube:
With a razor blade, cut the tube off leaving only the rim
that the cap snaps into.
Put your sample in the depression in the middle of the cap (inside).
cover with membrane and snap the rim down over it.
(I have done this but
On 09/27/2014 08:32 AM, Mark J van Raaij wrote:
Hi Rohit,
you should really ask Phenix questions on the Phenix bulletin board...
Hey, some of us run Phaser from the CCP4i gui!
(Otherwise I agree with the advice)
On 27 Sep 2014, at 13:34, rohit kumar wrote:
Dear All,
.
.
1. what is the 3-letter code (residue type) of your heme? Ligand Explorer shows
maybe half a dozen ligands for heme. Most notable HEM (protoporphrin 9 with Fe),
HEC (same but with the double bonds in the vinyl substituents saturated) and
HEA (heme a). There is even an entry for the
(Don't know if this should go to developers or the list. Some users may have
more information, or be interested in the information.)
I'd like to point out what i believe to be errors in the HEC.cif file released
with
CCP4 version 6.2 and later.
HEC is heme c which is regular heme as in
On 08/15/2014 09:40 AM, Faisal Tarique wrote:
Hello everyone
Can anybody please tell me where to locate the Corelation value between half
sets (CC1/2) of a data processed through HKL2000 ??
First of all you must have a recent version of the suite- it didn't exist in
earlier versions.
Then,
Thermo scientific has air/water chillers. Google:
thermo scientific neslab merlin recirculating chillers
brings up the links.
We have one of these cooling an Oxford xcalibur.
It supplies circulating cold water under pressure which
we hook up where the house chilled water would go on
the
So on second thought, practically speaking I guess observed is all,
since we never see the ones that are rejected by the -3 sigma
observed criterion
On 07/15/2014 12:44 PM, Edward A. Berry wrote:
I don't think observed means all the reflections that were integrated,
becasue one of the other
The plane will scatter, and all atoms in the plane will scatter in phase
if angle of incidence equals angle of reflection. this is how a mirror
reflects. Furthermore all the parallel planes will also reflect at this angle.
Trouble is the beams scattered from the different parallel planes are
17:05, Edward A. Berry wrote:
I see, L-dopa is a phenolic (o-quinolic actually) compound, same as what gets
oxidized
in sliced apples to turn them brown.
At least, that's the way it used to be.
http://www.okspecialtyfruits.com/arctic-apples/about-our-nonbrowning-apples
Truly nonbrowning Arctic
On 06/16/2014 04:26 PM, George Devaniranjan wrote:
Hi everyone,
I apologize at the beginning itself as I am new to using PHENIX/X-ray
crystallography so this question might not make the most sense but I will try
and explain it well.
I cut out a part of a map for a PDB fragment using phenix
But, if you convert to structure factors and recalculate the map in a different
cell,
the features will be stretched to fill the cell, which I take it is the
original problem.
I found Kleywegt's RAVE package very convenient for doing this,
but i believe the functionality is now available in
If you refine crystal mosaicity (I assume there is a way to do that in the
gui)
then scalepack prints out a single value for the crystal (search the logfile
for mosaicity)
eab
On 05/16/2014 12:07 PM, hongshi WANG wrote:
Dear all,
Thanks for all your reply and useful comment on this.
Harry,
On 05/07/2014 10:52 AM, Tim Gruene wrote:
At 2.5A resolution (the resolution this thread is about)
But maps ae not made at 2.5 A but from say 30A to 2.5 A.
In principle (i.e. if the 0,0,0 reflection were used), the effect
of diminishing the amplitude of high resolution terms is not to
On 04/24/2014 08:33 AM, Phoebe A. Rice wrote:
If you are doing real-space refinement of the entire model against a map in
coot, isn't it also important to make sure that the Rfree reflections were
NOT used in calculating that map? Depending on how the map was made, that
info can be hidden
but using fill-in when calculating the map- replace the free reflections not
with
the measured values, or with zero, but with the value calculated from the
previous model.
Such an approach has been reccommended for density modification with R-free.
eab
On 04/24/2014 09:58 AM, Edward A. Berry wrote
There are three places in a pdb file where resolution is defined.
Unfortunately by current conventions I believe they are all required
to show the same value. If one of them could be redefined to be
effective resolution, with a comment to explain how that was
arrived at, it would take the
Roberto Battistutta wrote:
Hi,
in the Rupp book the following relation is reported (on pag 415):
Rmerge ≈ 0.8/I/σ(I)
referring to a relation of the linear merging R-value with the signal-to-noise
ratio.
in a 2006 CCP4bb, Manfred Weiss reported:
Rrim (or Rmeas) = 0.8*sd(i)/I
Bernhard Rupp
After deposition (my experience is with RCSB) you will get back a processed
file to verify. See how the waters have been renumbered, and renumber
in such a a way that your original scheme is easily identifiable but in
keeping with whatever the renumbering was trying to achieve- e.g. your
waters
Encouraged by recent help from the BB in filling in gaps in my
understanding, maybe I can get help with another question:
At the top of page 121 in Blundell and Johnson, it is written:
The total wave scattered by a small unit of volume dv at a position r relative to the
wave scattered from the
I think I can agree with all of that. Thanks for helping me work this out!
Ian Tickle wrote:
We come up with the same conclusions with our different ways of thinking
about it:
for one, deriving the concatenated simple operators to represent a general
rotation,
and the
, that is irrelevant and not helpful to my understanding.
Tim Gruene wrote:
Dear Ed,
On 03/31/2014 08:55 PM, Edward A. Berry wrote:
[...]
Looking at the math, it depends whether you multiply from right to left
or left to right
x' = Rz(a) Ry(b) Rz(g) x
or
x' = Rz(a) (Ry(b) (Rz(g) x
, Edward Berry ber...@upstate.edu
mailto:ber...@upstate.edu wrote:
Thanks, Ian!
I agree it may have to do with being used to computer graphics, where x,y,z
are fixed
and the coordinates rotate. But it still doesn't make sense:
If the axes rotate along with the molecule
According to the html-side the 'visualisation' includes two
back-rotations in addition to what you copied here, so there is at
least one difference to the visualisation of the Eulerian angles.
Right- it says:
This can also be visualised as
rotation ϕ about Z,
rotation ω about the new Y,
Neat! How do you control the depth (front of slab to back of slab)?
FOOS Nicolas wrote:
Hi Remi,
you place the pointer (pink cube) at the place where you want put the atom.
After you click on Place atom at pointer (yellow square with blue cross).
HTH
Nicolas
axe, you replace the pointer at the right place and again 90 along Y, you
replace and it should be good.
Finnaly, you have to turn your model in different position and replace the
pointer at the right place.
De : Edward A. Berry [ber...@upstate.edu
And include FAD at a few uM in your column buffers. Although if you are getting
two separate sharp peaks for protein and FAD, it doesn't sound like it is
bleeding
off during chromatography but rather already dissociated in the material you
apply
to the column. Take a spectrum of the material in
Evans
Edward A. Berry writes:
Edwin Pozharski wrote:
I just want to point out that what is requested upon uploading data to
the
Protein DataBank is
NET I OVER AVERAGE SIGMA I
To me it sounds pretty much like I/sigmaI.
Yes, ADIT asks
Eleanor Dodson wrote:
Jim's point is that SigI is manipluated in the program, and its value
reflects the
programmers ideas. If you want to make your hair stand on end process the
same data with
SCALEPACK and MOSFLM and get the Riso between the 2 SIG estimates! 50% on a
good day is
Mark A. White wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
I have a couple of simple awk commands that will calculate both I/sI and
Redundancy, by
parsing the the scalepack output log.
### I/sigma
phenix.merging_statistics gives it also. And I think a recent post by Z.O. indicated the
current version of the HKL suite gives I/sig(I) and new statistics including CC1/2 or CC*.
Jacqueline Vitali wrote:
Phil Jeffrey has a small program to calculate avg. I/sig for Table 1 including
for
Govindjee and Fork's biography of Stacey French is available here:
http://www.nasonline.org/publications/biographical-memoirs/memoir-pdfs/french-c-stacy.pdf
or if your library subscribes to photosynthesis research,
http://link.springer.com/article/10.1007%2Fs11099-006-0041-6
Mark J van
Or if the tip is hopelessly pitted you can get a new one (for a Branson 1/2
inch horn) at:
http://www.proequip.com/productlist.asp?pcid=31
(thanks to:
http://blogs.cornell.edu/collinslab/2010/04/12/time-for-a-new-tip/ )
Reza Khayat wrote:
A lot of ageing sonicators are not really ageing. Have
You can use extend (now mapmask) to extend a map containing at least the ASU to arbitrary
dimensions
#
fft \
hklin in5s.mtz \
mapout temp.map \
EOF-fft
TITLE fft map
RESO $LORES $HIRES
LABIN F1=FP F2=FC PHI=PHIC
SCALE F1 2.0 0.0
SCALE F2 1.0 0.0
FILLIN
If the pK's are well separated, so that only one is titrating at a time ( assume
only two species exist at a time), the number of equiv of NaOH to add would be :
1/(1+10^(pK1-pH)) + 1/(1+10^(pK2-pH)) + 1/(1+10^(pK3-pH))
where each term transitions from 0 to 1 as pH passes through it's pKa
In
The kinase domain of FAK can be made constitutively active by a mutation
and expressed in E. coli. It's called Super FAK Kinase. But i am afraid
it is rather specific. If you don't get a better lead I can send you the
sequence and a reference.
Gloria Borgstahl wrote:
Does anyone know of a good
wrote:
Hi Graeme,
There was a CCP4BB thread about this quite recently (14th Nov 2013). I've coped
below
responses from Edward Berry and Matthew Franklin.
SCALA AIMLESS have no sigma cutoffs, but TRUNCATE does. According to the
documentation,
reflections with intensities less than minus 4 standard
(assuming of course the .doc files aren't also missing).
CDOC: Undefined variable.
[berry@sbserv ~]$ ls $CCP4/doc
ls: cannot access /sw/lnx/ccp4-6.4.0/doc: No such file or directory
I second the request for continued man pages and .doc files
Ian Tickle wrote:
I agree completely with Tim: I
As I understand it this refers to the decision whether an observation is valid or not, and
the default value in HKL suite is -3 sigma (note the negative sign). The
denzo/scalepack manual explains that while it is important not to exclude
observations
that are slightly negative due to random
You may also have to change your grid for the fft (resampling in photoshop parlance).
From the sfall documentation:
Different spacegroups have special requirements
for factorisation. No prime factors higher than 19 are permitted (The
`atom map' generated on this grid has the asymmetric
Is there a server or program to predict binding sites for monovalent metal ions?
Ideally should work with just the protein structure, but a program that sorts
through
the waters in a high resolution structure and tells which are likely to be K+
or Na+
would also be of interest.
Ed
/gerard/rama_server.pl )
One could also identity potential metal ions within COOT as well.
HTH,
Best Wishes,
Partha
On Fri, Nov 8, 2013 at 9:09 PM, Edward A. Berry ber...@upstate.edu
mailto:ber...@upstate.edu wrote:
Is there a server or program to predict binding sites for monovalent metal
I liked Ian Tickle's 1-line ccp4 script for changing the space group with
mtzutils.
I believe CAD can do this also. In any case, there's no need to reprocess.
Some reflections present in the current data will be systematically absent in
the new space group, but presumably they will be eliminated
constant...
On 3 Nov 2013, at 12:50, Edward Berry wrote:
Looking at it from the other side- suppose we say for a robust refinement we
need a
certain number of reflections- say 4 times the number of atoms, maybe less, I
don't
know. Any more than that is not really going to affect the structure, So
I wonder if there is a big difference between dehydrating in a drop, where the amount of
mother liquor is essentially unlimited, and dehydrating a mounted crystal in something
like the FMS, where there is only a thin film of ML on the surface. In the latter case,
once the surface fluid is gone,
Pro-Origami ?
pdbsum ?
Ashu Kumar wrote:
Dear all,
I am sorry for a non-ccp4 question. Does any one know of a server/program which
can be
used to draw the secondary structure elements e.g. If I specify 1-50 loop,
51-100 helix,
101-120 loop...like that...I have secondary structure prediction
No, my mistake, those require a structure.
If you have only sequence and predictions, I think TopDraw would be ideal.
Edward A. Berry wrote:
Pro-Origami ?
pdbsum ?
Ashu Kumar wrote:
Dear all,
I am sorry for a non-ccp4 question. Does any one know of a server/program which
can be
used
BAL (British anti-lewisite?) is supposed to destroy the FeS2 Rieske cluster in
complex III
Don't know how general it is.
Yuri Pompeu wrote:
Dear Community,
I apologize for the off topic question but it is hard to resist since so many
of our colleagues are incredibly knowledgeable.
I am
Gloria Borgstahl wrote:
Hello ccp4ers,
I am helping a colleague develop a grant and have a vague recollection of
structures of
transmembrane protein receptors that signal across the membrane. Can anyone
send me
specific examples?
Many thanks, G
I think cytoplasmic and periplasmic domains
. This is the kind of information we use to calculate our
wonderful electron density maps.
Best,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Edward
A. Berry
Gesendet: Freitag, 23. August 2013 01:01
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re
Along the same lines, does anyone have a program for converting Raster-3D format
such as Molscript puts out, into one of the formats readable by a 3D printer?
eab
Ronnie wrote:
An off-topic question-now that 3D printing is becoming more common, has anyone
tried to print protein structures
out VRML format files.
Sometimes you need add additional 'struts' to give additional structural
support, Jmol has option of adding these struts.
best regards,
Joel
On 23 Aug 2013, at 21:33, Edward A. Berry ber...@upstate.edu
mailto:ber...@upstate.edu wrote:
Along the same lines, does anyone
chokes trying to process the file.
Cjeets,
Artem
On Aug 23, 2013 5:54 PM, Edward A. Berry ber...@upstate.edu
mailto:ber...@upstate.edu wrote:
Thanks, yes, i should have checked out the link on the original post before
asking.
Free programs blender or meshlab convert vmrl to .stl files
herman.schreu...@sanofi.com wrote:
Dear James,
thank you very much for this answer. I had also been wondering about it. To
clearify it for myself, and maybe for a few other bulletin board readers, I
reworked the Bragg formula to:
sin(theta) = n*Lamda / 2*d
which means that if we take n=2,
it by
this new thread – does this makes sense?
Gregg
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A.
Berry
Sent: Thursday, August 22, 2013 2:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d
)
Ethan Merritt wrote:
On Thursday, August 22, 2013 02:19:11 pm Edward A. Berry wrote:
One thing I find confusing is the different ways in which d is used.
In deriving Braggs law, d is often presented as a unit cell dimension,
and n accounts for the higher order miller planes within the cell.
It's
Would you happen to know what the A280 of a 1M (or .1 M) solution is?
I wonder if this absorbance is really due to impurities or is the tail of a weak absorbance band of imidazole itself. I
notice A280 is not one of the properties sigma lists for its imidazole.
Jan wrote:
Hi Bernhard,
this
in absorbance above the background signal allowing
quantitation of your protein. The absorbance of imidazole can vary
depending on its source and purity, but elution buffer containing 250
mM imidazole usually has an A280 of 0.2–0.4.
Cheers,
Ed.
On Wed, 2013-08-21 at 11:25 -0400, Edward A. Berry
Great! and (oops) now I realize what I meant to say was compare cc* with
cc-work and cc-free.
eab
Nat Echols wrote:
On Wed, Aug 14, 2013 at 10:31 PM, Edward A. Berry ber...@upstate.edu
mailto:ber...@upstate.edu wrote:
If you refine once in phenix you can use phenix.cc_star to calculate
But it is highly unlikely that sum(I) in the denominator is zero if I/sig(I) is 2 as reported (providing the sig(I) is
valid- what was chi^2 in the last shell and overall?).
I sort of disagree that R-merge values over 1.0 are meaningless, provided not too far over. Granted R-meas is more
It's not ideal but we have been using a program called XtalDraw on windows for this, to display the different lattices
and to build up the content of the unit cell from a small molecule of 2 or 3 atoms by applying the different space group
symmetries. The students can edit the coordinates file
. As I remember,
GE healthcare's SEC manuals has recommended procedures on TP determination.
Zhijie
-Original Message-
From: Edward A. Berry
Sent: Saturday, June 29, 2013 7:43 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] off topic: good peak on gel filtration
Peter Hsu wrote:
Hi all
Engin Özkan wrote:
Also, why would we be using the batch-wise I/sigma's for determining
resolution cutoffs?
Agreed. For cutoff I guess it should be the final sigma going into the refinement program that matters, irrespective of
whether that was achieve by averaging more images or using a
@JISCMAIL.AC.UK] Im Auftrag von Edward
A. Berry
Gesendet: Sonntag, 7. Juli 2013 22:21
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] help identifying ligand
In a structure I'm refining, there are a couple of oblong blobs associated with
carboxylates.
(screenshots at http://sb20.lbl.gov/berry/ccp4/azide/)
If I
In a structure I'm refining, there are a couple of oblong blobs associated with
carboxylates.
(screenshots at http://sb20.lbl.gov/berry/ccp4/azide/)
If I modeled with two waters, they refine too close together for normal H-bond,
2.3 to 2.5 A; and their density is connected.
I considered one
Right-click on the shortcut on your desktop, select properties, and see what
folder
it has for start in. Try changing it to C:/CCP4/6.3/bin/ if it is not.
Or add that folder to your path.
Perhaps windows has a notion of current directory and
includes that in the search path, and when you start
Peter Hsu wrote:
Hi all,
I've generally always thought as long as the peak was symmetrical and not too
broad would suggest a good sample. However, looking at my previous runs in the
past, I've had peaks as narrow as 1.5-2mL on a 24mL SD200, or slightly broader
peaks with about 3mL (all
a
standard sample and calculate the TP based on the peak shape. As I remember,
GE healthcare's SEC manuals has recommended procedures on TP determination.
Zhijie
-Original Message-
From: Edward A. Berry
Sent: Saturday, June 29, 2013 7:43 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] off
Somewhere I got the idea that a diffractometer is an instrument that measures one reflection at a time. Is that the
case, and if so what is the term for instruments like rotation camera, weisenberg, area detector? (What is an area
detector?).
Logically I guess a diffractometer could be
:
Dear Ed,
to me, an '-ometer' is a device that measures whatever you put in
front of the 'o', so in case of a diffractometer that's a device
that measures diffraction.
Best, Tim
On 06/19/2013 08:11 PM, Edward A. Berry wrote:
Somewhere I got the idea that a diffractometer is an
instrument
Is Ethan Merritt's anomalous scattering page at:
http://www.bmsc.washington.edu/scatter/
down or moved, or the firewall I'm behind is blocking it?
I want to check feasibility of a native-iron MAD experiment,
and I'm not very good at math.
thanks,
eab
of anomalous scatterers, and
it tells you how accurate your data has to be to make the
anomalous signal significant.
Thanks,
eab
Bosch, Juergen wrote:
seems to be down sorry.
you should be able to use crossec from ccp4
Jürgen
On Jun 1, 2013, at 6:47 PM, Edward A. Berry wrote:
Is Ethan Merritt's
-links.html?sfvrsn=0
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. Berry
[ber...@upstate.edu]
Sent: Saturday, June 01, 2013 6:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] anomalous scattering server down?
Hmm- looks like
] on behalf of Edward A. Berry
[ber...@upstate.edu]
Sent: Saturday, June 01, 2013 6:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] anomalous scattering server down?
That's what I wanted. Results are not promising- Bijvoet differences
would be less than 2% at peak, and this is not lysozyme.
Thanks
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