Dear Urmi,
My first question, did you collect a full data set at a synchrotron and
processed this data? I think your diffraction is not as bad as you think it is,
and you may get 3-3.5 Å data from it. I asume the crystal structure of the
antigen is known and even with 4.5 Å data you could run
Deav Kavya,
The acetate is probably conformationally disordered. I would examine the
electron density maps to see if there might be an alternative orientation. If
so, you could model this and with occupancies around 0.5 your validation
problem would be solved and your model would probably be
Hi Wei,
if you tried both P3 and P6 and all subgroups, the right space group should
have been in there. By the way, the number of monomers in the a.u. will depend
on the exact space group (e.g. 1 in P622, 2 in P6 or P321, 4 in P3). There
might be a conformational change, which causes the MR
Dear Bulletin board,
I am looking at protein complexes with ligands containing non-natural amino
acids. When I run PISA, I get the total area of the ligand, as well as the area
of the ligand-protein interface, but hydrogen bonds and salt links are not
recognized. I therefore do not think the
Hi Supratim,
if both the crystal and Mass spec tell you that you have 6k and 13k fragments,
proteolysis definitively took place. There are several possible explanations
for the phenomenom you observe:
-time: processes that do not occur during the few hours of a normal biochemical
experiments,
Dear Faisal,
I might be missing something, but why not ask the annotator instead of the
bulletin board? He should know which value is meant. For me, a sigma belongs to
a set of observations or parameters and without any further information one can
only guess (as Ed just did) which set. My
Dear Pramod,
in addition to what has been said already, a few comments from my side. From
what you write, the first thing I would do is to check the basics:
-Is the protein that crystallized the protein you think it is? Plasmids do get
mixed-up and sometimes a more abundant natural protein with
Dear Bulletin Board,
Prodded by pdb annotators, which are very hesitant to accept coordinate files
when their Rfactor does not correspond with our Rfactor, I had a look again
into some old data sets, which I suspect are twinned. Below are the results of
some twinning tests with the Detwin
Dear Mitch (and Philip and Phil),
It is clear that I should give refmac a go with the non-detwinned F's and just
the TWIN command.
Thank you for your suggestions,
Herman
-Ursprüngliche Nachricht-
Von: Miller, Mitchell D. [mailto:mmil...@slac.stanford.edu]
Gesendet: Donnerstag, 20.
Dear Bulletin Board,
After some headbanging (Refmac5 had helpfully created gap records for all
insertions and deletions present in the structure), I got refmac5 running with
the TWIN option. Refmac5 also found the k,h,-l domain and rejected the other
possible domains because they were too
Hi Robbie,
That is what I tried. The Rfactor got a lot worse (14%-18%) and the Rfree got
a little worse (by 0.1-0.2%). My feeling is that that is not the right
approach. Roger Rowlett suggested to give PDB_REDO a try. Maybe you have some
instructions available how to get a local version?
Dear Tim,
I normally do not use Refmac, so I have no idea what to expect and what would
be a good weight. I will do the molprobity test, but I do not expect major
problems. This is a MR structure with a high resolution search model with 100%
sequence identity. A few amino acids may have
Dear Ansuman,
It is not entirely clear to my what kind of answer you are expecting. As Tim
mentioned, from the B-factor formula, one can derive an estimate of the
deviations of atoms from their average positions. This should give some idea of
the inherent flexibility of the protein. From my
Dear Pramod,
To run XDS, you could try to run it via the CPP4 procedure XIA2, or via
autoPROC from Global Phasing. What also may help is to retype the line:
NAME_TEMPLATE_OF_DATA_FRAMES=../images/WFTig1_???.mar2300 ! MAR345
I have had cases, where there were (I believe) hidden characters in
Dear Rain,
Insertion codes are still a sore point for many CCP4 programs and one of the
reasons I prefer Buster over Refmac. Refmac5 does not remove insertion codes so
I suspect the problem was with autoMR. The easiest is to superimpose your
search model with insertion codes onto the pdb file
Dear Francois,
I also prefer not to use insertion codes. However, for certain protein families
(serine proteases, antibodies), vast amounts of literature exist using amino
acid numbering schemes with insertion codes. By creating a new numbering scheme
without insertion codes, one would create
Dear Jiang Yan,
The Matthews function is based on an average protein crystal with 50% solvent.
However, crystals do exist with as little as 25% solvent or as much as 75%
solvent, so if your structure refines to an Rfree of 20%, your structure is
solved and you have a crystal with a high
Hi Rhys,
Since I did not see a reaction on the BB a few comments from me.
The first is that it never hurts to grow better crystals. Life and the referees
will be much easier.
The good news is that it is often possible to get surprisingly useful data from
badly looking diffraction images.
Dear Ed,
What is the pH of your crystallization buffer? If it is acidic, either the
azide or the carboxylate may be protonated. Also the local environment of the
carboxylate can make a hugh difference in PKa. You could also use some Bayesian
logic: given the elongated linear density, what else
Dear Ed,
For me, 3 mM is a significant concentration. If you have another crystal left,
you could transfer it to a storage buffer without azide and collect a data set
and see if the density disappears. A very small molecule, non-covalently bound
on the outside of the protein should disappear
Dear Marc (and BB),
I guess as usual, in real life the obvious is less obvious as it seems to be.
I, and I guess many of my colleagues trying to find new drugs, have quite a few
protein-inhibitor complexes where the inhibitor formed a covalent link with
e.g. the active site serine. In these
Dear Stefan,
Did you have a look at the NCS related helices? To me it looks like your NCS
restraints on B-factors are too strong, or not valid for your crystal packing.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Stefan
Dear Monica,
Having gone through all the efforts of purifying the protein, growing crystals,
collecting and processing the data, running molecular replacement (asuming you
intend to solve the structure that way) is trivial and you should try it in any
case.
But:
Your data does not look great.
Dear Ting Wei,
For me, your problem breaks down into two parts:
1) What do you want to do?
2) How can you do it?
Since you already have a hypothesis, I would write down the mathematical
formula of the calculation you would like do. In the internet, you should be
able to find the formula's you
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, for the same sin(theta) d becomes twice
Dear Edward,
Now I am getting a little confused: If you look at a higher order 2n
reflection, you will also get diffraction from the intermediate 1n layers, so
the structure factor you are looking at is in fact the 1n structure factor. I
think your original post was correct.
To summarize how
A trick I like is just to freeze the reservoir solution or would-be
cryo-solution without a crystal present. If the frozen solution stays clear and
does not show ice rings on e.g. a home source, it is worth trying. Otherwise,
the solution needs optimization.
Herman
-Ursprüngliche
Dear Enrico,
You are right that the trick has its limitations and I am aware of it. However,
it might not be as bad as you think. Fiddling with the crystallization buffer
or transferring crystals to different buffers also causes stress to the
crystals and in many cases loss of resolution. If
Dear Yu,
before we can make suggestions, we need to know what the problem exactly is.
Did the data process ok with HKL2000 and not very good with XDS, or did the
data not process very well with both programs and are you comparing with
previous data sets from different crystals?
XDS is very
Dear Jan,
since electrostatics go with one over distance-square, there may still be some
electrostatic repulsion if the aspartic acid is further away as the arginine.
Another question is, what happens with the arginine of the ligand in absence of
the antibody? Does it then make a salt bridge
Dear Lucas,
I recently came accross a scientific comment on the 1.9 Å PDB structure 4i8e,
where apparently a HEPES molecule had been misinterpreted as a disaccharide.
See Ives Muller, acta cryst F96, 2013:1071-1076.
Best regards,
Herman
Von: CCP4 bulletin board
Sorry, it is acta cryst F69, not 96!
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
Schreuder, Herman RD/DE
Gesendet: Donnerstag, 17. Oktober 2013 16:11
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] AW: [ccp4bb] Problematic PDBs
Dear Lucas,
I recently came accross
Dear Stefan,
The picture you give of your crystals is indeed quite messy. The first thing I
would do is to sort all the information at hand and try to see what could be
going on. Based on the (limited) information you give, I have to following
comments:
1) Autoindexing suggests a
Dear Jan,
There are a few things a would do in this case. The first is to check the
processing to make sure the space group is really C2 and, although unlikely,
not some other space group.
The second thing would be to try to place the first component. From your email
it is not clear to me
Dear Stefan,
Congratulations! It seems that you not only have pseudo-translation and pseudo
4-fold symmetry in your diffraction, but also pseudo 8-fold symmetry in your
protein molecules! An excellent case to learn a lot about space groups and NCS
symmetry.
3) you are right, you might see
Dear Sangheon,
there is no law that forbids P21 crystals to have a~b~c and beta~90°. It only
does not happen very often. So your solution can be correct. You may want to
analyze your crystal packing with ccp4 program Zanuda, to see if a higher
symmetry space group could be used.
Best regards,
Dear Thuy,
I would try to model alternative conformations. E.g. blob2 looks like a lower
occupancy cadmium ion coordinated to the glutamine, causing the histidine to
assume an alternative conformation, also coordinating the ion. Just try to
build different possibilities. If, after refinement
Sorry, I meant glutamate.
HS
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
Schreuder, Herman RD/DE
Gesendet: Donnerstag, 31. Oktober 2013 09:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] AW: [ccp4bb] help with strange density map
Dear Thuy,
I would try to model
Dear Thuy,
For blob1 you should also try to fit alternative conformations. Your maps are
good enough to give you a fair chance. You should also look for reasons behind
these alternative conformations: has a neighboring disulfide bond partially
opened? Is there a partially-occupied cadmium
Dear Fulvio,
you cannot detwin perfectly twinned data with this formula. The term (1-2α)
becomes zero, so you are dividing by zero. With good refinement programs
(ShelX, Refmac), refinement is done against twinned data, which is better than
to detwin the data with the formula you mention.
As I
Dear Fulvio and others,
I do not understand this whole discussion. In case of perfectly twinned
crystals, it is impossible to derive a detwinned F1 and F2 from two
independent, but otherwise identical measurements. In this case, the only
signal is noise, and one could as well use a random
Dear Niu,
To me, it looks like random density. Since coot contours are based on sigma
levels, you will always see features. I do not think you can do anything with
your current map. As others have said, it is always a good idea to test ALL
possible space groups, even if you are convinced it is
Dear Monica,
strong 222 rotational symmetry plus translational symmetry would give 8
molecules in the unit cell. (4 in the a.u. in P2x and 2 in case of P2x2x2x).
(test ALL options!).
Do you have models for both the ligand binding domain, or only for the DNA
binding domain? You have to search
Dear Dmitry,
I only work with N-glycosylated proteins and here the people from coot and
refmac have done a wonderful job in creating all necessary dictionaries. I
would be very surprised if this would not be true for O-glycosidic bonds.
Instead of reinventing the wheel myself, I would first
Using your favorite editor, you can copy the LINK record from the pdb file
generated by Coot and paste it into the pdb file produced by Phenix. You can
also make a script to do this. This is what I did during the time LINK records
were not properly handled by coot, refmac and buster.
Best
Dear bulletin board members,
A referee came back with a question about the accuracy of refined
group-occupancies. In the manuscript we describe 3 crystal structures with
resolutions between 2.1 and 2.4 Å. In all three cases, the inhibitor has been
fitted in two alternative conformations and
Yes.
First create in coot alternative conformations for the residues in the loop.
Use the split all of a single residue option. This is the default. Then use
the rotate/translate zone option to move one of the conformations to the
alternative position. For this you have to select the first and
Dear Acoot,
if your metal is part of a protein crystal, your diffraction image still looks
like the diffraction of a protein crystal. If you see salt spots, your crystal
is salt, not protein.
However, what sometimes happens is that one has a badly diffracting protein
crystals with some tiny
Dear Prem,
90-95% completeness is not great, but definitively acceptable und should not
stand in the way of solving your structure by MR.
I guess the XDS statistics you mention are from the highest resolution shell?
Otherwise they would be bad. To be sure you processed the data correctly, the
Dear Nazia,
you give very little details, so it is difficult to give a specific advice.
Here are some comments:
-How high is your Rfree? Depending on the resolution of your data, an Rfree in
the 25-30% range while not good, may still be acceptable.
-Are there problems like ice-rings in your
My first guess was also a metal ion. However, a tryptophan as Fred suggested
cannot be ruled out. A simple preliminary test is to scroll up the contouring
level and look when the contours of the blob disappear. If the contours quickly
disappear, you have something disordered or light. If the
Dear Priyank,
At 4.5 sigma, it is definitively something heavy like a gold ion.
The red sphere of difference density around the ion is most likely caused by
the fact that the ion has partial occupancy, which was not refined. In these
cases, refinement programs try to compensate for partial
Dear bulletin board,
I recently submitted a coordinate file to the pdb that had been optimized with
pdbredo, which used TLS refinement. All TLS parameters are in the header, but
the pdb wants these to be converted to ANISO records. I did a google search and
also looked into Tlsanl, but did not
Dear Ian,
Thank you for this information. It worked! This useful feature is, as you said,
not included in the documentation.
Also, I made the mistake to use the ccp4 gui to run Tlsanl. Not only would the
gui insist that I had to provide a .tls file, when I left the space for the
.tls file
Dear Wei,
I would put something big in the binding site like a tryptophan, to physically
block access of the ligand. Check beforehand in coot if and at which position
such a residue would fit best.
Best, Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Wei Shi
Dear Bonsor,
I fully second James suggestions but have a few additional comments:
If you get a solution in P6522 with one molecule, you should get the same
solution in P65 with 2 molecules. One of the crystallographic symmetry
operators would then be non-crystallographic.
The current version of
Looks like you need to search for more molecules.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Amanda
Blythe
Gesendet: Montag, 16. Dezember 2013 11:46
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Phaser output problem
I am trying to solve a structure by
Dear Alastair,
Since there does not seem to be a compelling reason to use P 32 to describe the
contents of your unit cell, I would use P 32 1 2. Refining a structure in a
lower symmetry space group often gives slightly lower Rfactors since the
refinement program has more parameters to play
Dear Shane,
Human antithrombin III (code 1ath) is a dimer of an active and latent
conformation.
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Shane
Caldwell
Gesendet: Montag, 27. Januar 2014 19:09
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Examples of
Dear Bert,
The first thing I would do is to calculate the Matthews number: Does at least
one monomer fit in the P622 asymmetric unit? If not, your crystals are
definitively twinned.
As mentioned below, I would also check the I^2/I^2 ratio, but I would do
it with the data processed in P6,
I would try Coot, setting a very large map radius and adjusting the depth
cueing with the d and f keys.
My 2 cents,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Francis
Reyes
Gesendet: Mittwoch, 12. Februar 2014 03:08
An:
By applying a high temperature factor, one should not suffer Fourier ripples,
since the missing high resolution reflections have negligible intensities, or
put differently, one simulates a poorly diffracting crystal.
Best,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board
Dear Carina,
An additional problem is that due to the dilution, but also due to the
separation of monomers and dimers you get a reequilibration which is dependent
on Kon/Koff of the interaction. Unless these are very slow, you cannot use size
exclusion to determine the monomer/dimer ratio.
Dear Lisa,
the first thing to check is whether the polymerization is due to disulfide bond
formation. If you run a gel of your protein with one sample boiled in the
presence of b-mercapto ethanol and one sample boiled in the absence of bME,
this should tell you whether disulfide links are the
If the ligand is a bona fide protein (more than a few amino acids and its own
stable fold), I would include it under protein. However it is a matter of taste
and, as Nat says, it will probably be dumped in the supplementary materials to
be never looked at again.
Herman
Von: CCP4 bulletin
Another option would be the merge molecules option in coot (calculate -
merge molecules). In coot you would also be able to move the molecules to the
same asymmetric unit if that would be necessary. However, depending on the
space group the MR solutions could have different origins and with
Dear Chris,
I have looked at the images. The 1.65Å data set seems to have a high mosaicity,
but to be otherwise ok. The 1.9Å seems to have one extremely long axis almost
perpendicular to the rotation axis. One should always try to have such an axis
parallel to the rotation axis during data
Dear Amlan,
The sigma of an Fo-Fc map map depends on the residual noise in your map. In a
well-refined structure, the sigma will be low, so at 3 sigma it will show very
weak features.
My guess is that your ligand is present in partial occupancy and that you will
find it in your 2Fo-Fc map when
In this case, editing the pdb file is probably the best approach. However, my
favorite approach is Validate Difference Map Peaks. By pressing . (next
peak) or , (previous peak), one can quickly go through all problems (red
density) or unexplained peaks (green density). The pointer will be
Hi Jarrod,
I think these 5 helices are either slightly misplaced, or somewhat disordered.
How does the main-chain density look like? Do you see a discrete main-chain, or
is the main-chain blurred and does the helix look like a blurred cylinder? If
the main-chain is clear, I would take off all
Dear Chen,
I am not an expert on SAD and MAD. However, at this stage I would not worry too
much about density going through the 2-fold axis. There might be a sulfate ion
or some other buffer component present at that position, or it may just be an
artifact that will go away once the structure
Dear Nazia,
My first suggestion would be to take your crystals to a synchrotron. With the
same crystals, you may get a precious 0.5 Å resolution more.
Concerning the processing, I agree with Jürgen that the beam center is the most
frequent culprit. The second thing to do is to make sure that
Dear Laurie,
To me this looks like a textbook case of lattice translocation disorder:
depending on the hkl values, the spot are sharp or streaked. Searching for
lattice translocation disorder should give you enough relevant papers to get
you going. Since it depends on the space group and the
Dear Remie,
The first thing I would do is to download a random file form the pdb with
sugars attached and examine how the link looks like in coot and in an editor.
You could use e.g. (shameless plug) 4ci9.
The next thing to do is to check the link record you created. Here the
punch-card
Sorry, I made a typo. One should of course delete the O1!
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
Schreuder, Herman RD/DE
Gesendet: Mittwoch, 9. April 2014 09:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] AW: [ccp4bb]
Dear William,
The lowest resolution spots you can see tell you something about your cell
dimensions since the resolution cannot be lower than the longest distance in
your unit cell. If you see spots at 30Å resolution, you are pretty sure you
have protein crystals, if you only see spots at
Dear Joel,
I always tell our chemists not to include piperazine rings etc. in their
compounds because of this conformational mess, but somehow they do not seem to
listen. ;-)
Unfortunately, do did not tell us how and with software you auto generated your
cif file, so I can only give some
Dear Paul,
I find it difficult to predict when a pipirazine nitrogen will be sp2 and when
sp3, so I usually search the csd with the exact substituent at hand and
supposed that Joel will have done the same. In general, I find that auto
generate programs are overly optimistic how far
Dear Joel,
I suspect that you will have a mixture of different puckers. Relaxing the
restraints would not be the way to go, since it might lead to a distorted
average structure.
If your cif file is correct (tetrahedral nitrogens), it should not impose a
specific pucker. However, you will have
Dear Faisal,
redundancy is total no. of observed reflections divided by no. of unique
reflections, i.e. how often each unique reflection has been measured on average.
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Faisal
Tarique
Gesendet: Donnerstag, 17. April
Dear Peter,
First a common misconception: your goal should be to get the best possible fit
of your model to your electron density maps. Rfree is only an indicator,
telling you whether you are moving in the right direction.
So in coot, you should look for places where your model does not fit
I would do a rigid body refinement, rebuild the structure and then go on with
refinement. To compare refined structures, you still need to superimpose them
first.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Faisal
Tarique
Gesendet: Donnerstag, 24. April
Dear Chen,
Twinning can be thought of as of two or more macro-crystals glued or grown
together. The reason that the reflections often overlap is that they share one
common plane from which they grow in different directions. Many twinning tests
are based on the fact that the two (or more) macro
Dear Ian and James,
Here I learned something new. I assumed that coherence length would be limited
by crystal quality, e.g. mosaicity and microdomains etc. which apparently is
not the case. For me, one of the characteristics of twinning is that there is
no interference between the twin domains.
Dear Sudarshan,
There are quite a few point to consider in MR:
-How good is your model? At 50% sequence identity with your protein, it is
probably ok, around 25% sequence identity it may or may not work. If your
protein is of the same protein family with a similar biological function it is
It can be done with pymol:
In the box in the lower left corner is an item selecting residues. By
clicking on residues you can change it to atoms or C-alphas
When you now click on the appropriate active site atoms, you can select the
alpha carbons and a (sele) item appears.
In the (sele) item
Dear Rain,
Maybe a little late, but here are some more comments:
1) What is the deal? For me, one can only know the space group after the
structure has been solved. I have seen quite few cases (e.g. twinning,
non-crystallographic symmetry etc.) that all programs (XDS, pointless) and
Dear Matt,
95% solvent is highly unlikely, but not impossible. Did you have a look at the
crystal packing? Are there continuous crystal contacts in all three dimensions,
or are there layers of molecules that are not connected? Are you sure your
space group is P212121 and not one of the other
I am also in favor of two versions of the pdb: one archive version with all
models as originally deposited including retracted and corrected versions,
which are useful for educational purposes, and a curated version with only
models that meet a minimum of validation criteria, including credible
Dear Niu,
Provided you have a complete asymmetric unit (unit cell in P1), you could also
convert this map to structure factors and manipulate those, e.g. with sftools.
To calculate structure factors you could use sfall and also clipper has
utilities to convert a map to structure factors.
Dear Remie,
For reasons that probably only Garib understands, Refmac still uses LINKR
instead of LINK to link atoms. However (at least for Refmac) both LINK and
LINKR should work.
After a lot of complaining in the past (also from my side), the handling of
carbohydrates in Refmac is ok. I just
Jef,
PISA will give you the size of the protein-substrate interface, which is
inversely correlated to the solvent exposed surface. Subtracting the interface
surface from the total surface of the substrate will give you an estimate of
the solvent exposed surface.
Best regards,
Herman
Dear Lionel,
In case of a lipid-binding protein, we were able to remove most (90%) of the
bound lipids with a lipidex column. This could be verified by DSF since the
melting temperature of lipid-bound protein was ~6°C higher as the melting
temperature of the free protein. The delipidated
PS: if you are working with a human protein: most human proteins are quite
stable at 37°C (for obvious reasons).
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
Schreuder, Herman RD/DE
Gesendet: Freitag, 27. Juni 2014 09:21
An:
To get a rough idea of the solvent channels, one could use coot. By displaying
the symmetry molecules as Ca traces (an option hidden in the symmetry menu
under symmetry by molecule) one can set a large radius (100Å) and still
rotate the display. A more accurate display can be obtained by
Dear Bernard,
we once worked with a series of protease inhibitors which turned out to be slow
substrates, e.g. an acyl intermediate was formed that was subsequently
hydrolyzed. Here we had to reduce the soaking times to below 30 minutes,
otherwise we would see nothing, e.g. the large excess of
Nothing to get worried about. It means that other, equally valid choices of
axes may be possible (e.g. with polar space groups). Only if you want to merge
data from different crystals or if you want to scale native and derivative
data, you have to make sure that the same choice of axes is being
You might try some shrink-wrap.
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller,
Jacob
Gesendet: Montag, 7. Juli 2014 18:43
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] emergency substitute for RT loop cover?
Anyone
Dear Kenneth,
You should be able to find the information you are looking for in the logfiles
of your dataprocessing at the scaling/merging step. E.g. in the logfiles of
scala you will find Total number of observations and Total number unique. I
am sure Scalepack will produce similar output.
Dear Appu,
What is your problem? To me this crystal packing looks completely normal. If
you look for tetramers in space groups with 422 symmetry I am sure you will
find examples with a similar packing.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Appu
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