Hi Shen,
I agree with Eleanor that the split spots will cause worse statistics, but
should not be a reason for molrep to fail.
What I would do:
Molecular replacement with a resolution cut of 3 or 3.5 Å.
Process and run molecular replacement in P1. You may have some tricky
pseudo-symmetry. With
Dear HK,
I agree with Artem, I would put the ketone in the green density below in your
pictures and make a covalent link with the arginine. The single oxygen I would
put in the density currently occupied by the ketone and add one water there as
well. In your refined omit maps, the current
Dear HK,
In your case mass spec would be extremely valuable. Not only could it prove or
rule out a covalent link, it will also convince referees that the link is real.
There is clearly more density than the degraded product you showed. I would
also ask an experienced chemist if a link between
Hi Heng-Keat,
I had again a look at your electron density pictures and these were my
impressions:
1) the Arginine as fitted looks fully occupied. There are no hints for an
alternative conformations.
2) The fit of the ligand, although reasonable, is not extremely good.
It seems that the only
Hi James,
Did you ever try what happens if you set all the FOMs of e.g. 2vb1 to 1.0 and
calculate a map? If you are sure they are not measurement errors they should be
included in the map. I would expect some huge ripples, but maybe the "outliers"
compensate and you get a truly interesting
Dear Iracema,
Thank you very much for your hint of using CCP4i, I never use it but this time
I should have used it to find out how to switch off the tNCS. Unfortunately, I
cannot reach any of the phaser.cimr sites. I get the error message that our
proxy server does not react. I can reach the
Dear community,
I wanted to switch off the tNCS for a Phaser run, but could not find any Phaser
manuals online, explaining how to do this.
So I have two questions:
1. How do I switch off tNCS in Phaser and
2. Are there any phaser manuals online? I tried hard to find them using
Bing, but
Dear Chris,
The first thing I would do is to load the FFT map (not the mtz) in coot and see
how densities of both ligands compare in that case. Also in FFT, did you
calculate exactly one unit cell, or did you select a region just around the
protein? If you contour the maps in terms of RMSD,
Dear John,
Plants cannot walk away to a more favorable spot. They remain stuck where they
germinate, e.g. whether the place is sunny, shady, wet, dry, fertile, poor etc.
So plants compensate by having a lot of genes available to be able to adapt to
the particular spot where happen to be. And
Being denied a job because someone else published your research may make the
dance also somewhat less happy…
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Mark J
van Raaij
Gesendet: Mittwoch, 21. August 2019 11:48
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL]
Dear Flemming,
As Jürgen said, what happened? Did A deposit the coordinate file in the pdb,
but did not publish and did B take this coordinates and make a publication? Or
did B ask A for the coordinates to have a look at and then made a publication
without agreement of A? Did B hack the
PS, you also have to define an alternative conformation, but that you probably
already did.
Von: Schreuder, Herman /DE
Gesendet: Montag, 5. August 2019 17:55
An: 'Maria Håkansson'; CCP4BB@JISCMAIL.AC.UK
Betreff: AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to
Zn2+
Hi
Hi Maria,
Did you rotate the phosphate, or invert it? If you invert the phosphate, you
may get into trouble with the parameters. Although a phosphate is symmetric,
its oxygens have different names and inverting it leads to all kind of
problems, especially in a high resolution map which does
Hi Stephen,
What happens if you delete the CE methyl group and run a round of refinement.
Do you get a positive blob of difference density in between the two sulfurs? Or
looks everything pretty ok? In the first case you may indeed have some unusual
phenomenon, in the latter case, the methyl
Dear Marina,
Just an observation from my side: if you are able to process your data in P622,
there must be some 2-fold perpendicular to l, which would most likely be a
non-crystallographic or a twinning axis. Is there a NCS 2-fold in the P321 data
set you solved? If so, is it perpendicular to
Dear Kevin,
It could also be that you have a particular nasty combination of tNCS and
twinning. Given your packing problems in the ab plane, this would mean that
your 2-fold parallel to c is generated by twinning and that probably one of the
21 axes is generated by twinning as well.
With some
Dear Jonathan,
In these cases, I usually see positive difference density nearby, indicating an
alternative position for one of the sulfurs, i.e. the disulfide bridge was
partly broken. I am too lazy to fit these, but if you want to do a perfect job,
you might want to fit an alternative
For glass X-ray capillaries, we used a Styrofoam box with some cooling blocks
at room temperature to prevent any fast temperature changes, which may lead to
condensation problems. Of course, you should add some materials to protect the
capillaries and keep them in place.
Best,
Herman
Von:
Dear Sam,
I would remove the ice ring and reprocess the data. Ice rings may wreak havoc
with scaling so at minimum you have to redo the scaling.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Sam Tang
Gesendet: Donnerstag, 4. April 2019 11:01
An:
Dear Deniz,
In the past, I had similar problems caused by the fact that when the residue
was “known” to ccp4, it would use the cif file from the ccp4 library instead of
the cif I had created myself. You could check if this might be the case for
you. You find the cif files under
I agree. The data processing software might have been confused by the NC 2-fold
and thought that it was crystallographic and of course, after merging the data,
the NC axis will have been made “crystallographic” with superimposed A and B
conformations at 50% occupancy. In this case, reprocessing
Dear ???,
Do you have any ice rings (even hardly visible ones) in your diffraction data?
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von StrBio
Gesendet: Sonntag, 24. März 2019 05:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Refinement
ALL.
I
Hi Alex,
Kevin is right. To clarify things a little, you don’t have to use the symmetry
mate selected by the molrep program. You can take the symmetry mate that makes
the relevant biological interactions instead. No need to change the space group.
You have to delete the molecule that does not
Dear Ezequiel,
Be careful, it also happens that the asymmetric contains two half-dimers, with
the other half of the dimers being generated by crystallographic operators.
In this case it is not possible to rearrange the monomers such that the
asymmetric unit contains one biological dimer and
I agree, how can we punch an mmCIF file on these cards?
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Edwin
Pozharski
Gesendet: Mittwoch, 20. Februar 2019 16:19
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Mandatory mmCIF format for crystallographic
Ed,
I did understand your question correctly and (at least for ligands) the
procedure I and also Diana Tomchick described, worked. However, I just did a
test with both Refmac and Buster and it seems that these programs have now so
far been perfected that “errors” like this cannot occur
Dear Edwin,
I do not know whether your question has been answered already, but the answer
is simple: you have to define alternative conformations. Easiest is to generate
them in coot with the “add alternate conformation” option in the right panel.
You may have to delete the original unlabeled
For me it is easy:
If your crystal does not diffract, you have a problem with your crystal, which
is usually very difficult to optimize
If you have no crystal in your loop, you have a problem with fishing your
crystal, which should be much easier to optimize!
Cheers,
Herman
-Ursprüngliche
A long time ago, before siliconized coverslips became commercially available,
we used to siliconize coverslips ourselves. It is not really that much work and
unsiliconized cover slips should be very cheap. If you wish, I could try to
find back the protocol.
Best,
Herman
Von: CCP4 bulletin
Dear Philippe,
As Randy just pointed out, when twinning, pseudosymmetry and other pathologies
come into play, things really get complicated.
I agree with what you said but for the current problem, things may be more
complicated.
To summarize:
- "bona fide" twinning: there are two different,
Dear Lan,
Thank you for your compliment. I do not use Xtriage, so I did not bother
looking at the log files.
What I meant to say is that with twinning, the crystal has different
macroscopic domains where the molecules have different orientations, say one
domain with orientation A and one
Dear Donghyuk,
Unfortunately, everything is possible when NCS, twinning etc. get into the
game. I do not have answers, but some questions for you to think about:
- Do you really have 6 twinning operators, or only one operator and are the
other operators generated by (non)crystallographic
Dear Andy,
Best would be to convert the phaser angles (plus vector) in a matrix (plus
vector) and use this for your transformations. The phaser people should be able
to provide you with information how to do this, since they have to do it in
order to produce their output files. Alternatively,
I think Jacob is right. As long as protein crystals contain about 10% "dark
matter"* not accounted for in any model, we cannot fake a "true" electron
density map and it is then not surprising that an 2mFo-DFc map is closer to a
model-based fake map than a map based on experimental phases.
HS
Dear Markus,
I believe the strong assumption in the community is that a clear single peak of
appropriate Mw is a clear indication of pure protein, worthy intensive
crystallization efforts. Whether it is active is another question and this
should be measured.
For your analysis, it is not
To me, it looks like some intergrown salt crystal.
HS
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Sam Tang
Gesendet: Dienstag, 9. Oktober 2018 13:13
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Weird diffraction pattern
Dear all
Hello. We recently shot a
Dear Liang,
The first thing I would do is to look through your complete scan. ADXV has an
option to display a movie of all images. It might be that some regions of your
scan are very weak or otherwise bad. Merging these regions with good regions
will produce high Rmerges.
I would also check
Hi Kevin, Pavel and others,
Since it seems that so far nobody answered the primary question: “Is there any
sever available to create electron density maps for cryo-em structures?” So I
will do it. The answer is very simple: They do not need to be created, they are
available from the pdb!
To
Dear Kay,
I have looked at XPAND and it looks like it is part of the O-package. Do you
know if it can also be used stand-alone?
Best,
Herman
-Ursprüngliche Nachricht-
Von: Kay Diederichs [mailto:kay.diederi...@uni-konstanz.de]
Gesendet: Mittwoch, 1. August 2018 15:00
An:
Dear BB,
I know it has been discussed some time ago, but a google search did not come up
with anything useful.
I need a program which analyzes the bound waters and suggests whether a
particular water might be a chloride, calcium, sulfate, sodium or something
else. Preferably a program that
Hi Marilyn,
I have been struggling with carbohydrates in the pre Glyco module era, which
was *not nice*. However, the following strategy works reasonably well:
1) Get the XYP monomer with the "get monomer" command.
2) Move the XYP manually in its electron density. This can be very
Hi Shijun,
Unfortunately, it happens very often that a ligand (in your case
Chloramphenicol) does not bind to the protein in the crystal. If you look into
the twilight gallery, there is a large number of crystal structures where
people desperately tried to fit their precious ligand in what
Dear Nick,
Thank you for your reply. I am looking forward to test a new Pandda version
that is hopefully compatible with the latest CCP4 version.
Concerning the error messages: I think they are very useful for developers, to
trace back in the code what had happened, but not for users, who need
Dear bulletin board,
I am trying to run Pandda on a set of about 50 data sets. I asked our system
manager to roll back to CCP4 update 047 and by using unique and refmac, I could
fix the problem of a few missing low resolution reflections.
However, then Pandda crashes apparently during
Hi Bernard,
I found a script I made a long time ago which produces a native Patterson. I
tested it with our reasonable recent CCP4 version and it still works!
You have to copy the attached script to your linux directory and make it
executable (type chmod +rwx makpat).
To generate a patterson
Dear JiYG,
With an unknown number of 1000 aa monomers, you definitively have a challenging
project!
In that case, you will have to do some homework before running phaser:
1) The Matthews program should give you an indication how many monomers to
expect.
2) P2 is a very low symmetry
Dear JiYG,
Unless the tNCS has caused processing problems, Phaser should automatically
deal with tNCS and I would recommend to just give it a try. If it fails, you
could try more sophisticated approaches.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von ???
Hi Gihan,
I guess your XFEL data set consists of data of hundreds of micro-crystals with
only partials?
The first thing I would do is to ask the beamline people for the best strategy.
Since they (should) have tested the beamline, they are probably the best people
to ask.
Next, in the early
PS: If you have two different home-brewn ligands, you have to rename one of
them (pdb and cif), otherwise the same dictionary will be applied to two
different ligands. Also make sure your cif file is a dictionary and not just a
coordinate file.
HS
Von: Schreuder, Herman /DE
Gesendet: Montag,
Hi Colin and Michel,
In my experience, both refmac and coot will use the most recently read-in cif
dictionary and there is no need to try to find an unique identifier for each
new ligand one uses. The new dictionary overrides the old one. Finding a unique
identifier for each new ligand would
Dear Careina,
If you do not have coordinates, what do you have then? A sequence alignment? In
that case you can look at the %identity and %homology to see how well the known
structure fits the unknown structure.
If you do have coordinates in some other format generated by some modeling
Dear Raj,
The pdb will accept any crystal structure submitted to them. They do not have
editors and referees that refuse to accept crystal structures. In the worst
case, your structure may have validation problems and you will get questions
about it. But this will happen with published crystal
If you use coot with on the fly map calculation (e.g. you load an mtz and not a
map file), you do not need to transform the map. Otherwise I would recommend to
run one more round of refinement and produce a new map your usual way. This
will also get rid of any rounding errors due to the
Hi Jiri,
A low-tech solution that will certainly work, is just to manually show the
relevant distances. In coot under measure there is an option to show distances,
just by clicking on the two atoms involved.
Good luck!
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im
Dear Denis,
I would first superimpose both monomers to see if you can find a reason why one
subunit has a bound water and the other not, which would in general be flanking
side chains in (slightly) different positions. Next I would look for some
global differences between the subunits that
Dear Noguchi,
If I understand correctly, you have one protein with 8 identical repeats and a
few additional residues at the N-terminus that you cannot see in the electron
density map. This means, that the N-terminal repeat is different from the other
repeats and theoretically, you should
Dear Martin,
I use a script which invokes the coot command similar to what you describe with
--script mapcent added on the same line. The mapcent script is attached. You
can either go to a certain atom, or set hte rotation center in Å coordinates.
You can add whatever commands to the script to
Dear Radhika,
What reason does Xtriage give for declaring the reflections to be outliers? Too
weak, too strong, other reasons? As was mentioned before, what is the
resolution of your data? In cases like this, it is always good to have a look
at the diffraction images to see if there is some
Dear Jacob,
The big advantage of microscopes (whether using electrons or X-rays) is of
course that you 1) do not need crystals and 2) get phase information. However,
aligning an extremely large number of single molecule images is non-trivial and
this is the reason it is still very hard, if not
At the bottom line, it is the quality of the image, not only the amount of
pixels that counts. Adding more megapixels to a digital camera with a poor lens
(as some manufacturers did), did not result in any sharper or better images.
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin
In line with Dale's suggestions, I would suggest that you reformat your voxel
map into the format of an electron density map and look at it with coot. I am
sure it will look much better and much more like the electron density we are
used to look at. Alternatively, you could display an bona fide
Dear Mark,
It does happen, even that two crystals from the same drop (everything
identical) have different space groups.
Best,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Markus
Heckmann
Gesendet: Donnerstag, 9. November 2017
Dear Martin,
You could calculate an Fo-Fc map with the FAD having half occupancy. This
should bring out the "pure" difference density for your modified FAD, which
might be easier to interpret. You may have to try different occupancies, say
0.4, 0.45, 0.5, 0.55, 0.6 etc. to find the point with
My feeling is that all non-standard amino acids should be labeled HETATM and
that the overzealous introduction of TER cards by Refmac is the bad thing, but
I might be mistaken…
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Eleanor
Dodson
Gesendet: Dienstag, 7.
Dear Martin,
For well-refined structures with low residuals, +/- 3 sigma levels (the
standard coot contour levels) are very small on an absolute scale. How does
your 2Fo-Fc map look like? Are there really big holes in the FAD for the
missing atoms with almost zero 2Fo-Fc density?
As others
You are right. In this case, I would put some waters in it, refine and see if
the density gets any clearer. However, since from this perspective the density
is quite far away from the protein, it could be a very disordered PEG, which,
even at high resolution, might be impossible to fit.
Best,
Dear Abhishek,
To me, it looks like an alternative conformation of the peptide chain or maybe
even a conformational change with respect to the starting model. The peptide
chain does not look too well defined, despite high resolution electron density.
Best,
Herman
Von: CCP4 bulletin board
Dear Eleanor,
The method I proposed works for any amino acid, not just tyrosine. Having an
amide as a separate residue may sound strange, but is it exactly how our
chemists treat it as well.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Eleanor
Dodson
Dear Michael,
Did you ask Phaser to check for all possible space groups? There are still I422
and I4 you did not mention. If the space group that came out of Phaser is
different from the space group used for processing, subsequent refinement
programs may use the wrong space group from the
Dear GIA,
In addition to the anisotropy, I would also check your diffraction images and
make sure that there are no (even hardly perceptible) ice rings present.
Depending on how the data processing software handled this, they may cause high
Rfactors in the range you mentioned.
Best,
Herman
Hi Abhisek (and BB),
I use the attached cif file. It has an NH2 residue defined as a peptide and
gets automatically linked to the peptide chain in the buster procedure I use.
So if your last residue is Tyr 100, you add NH2 101 as a HETATM in the peptide
chain.
I have not tested it with Refmac
With a detector in swing-out position, one has to include the corners. Also,
why should one discard potential data during processing? Based on the
statistics, one can always discard data afterwards if it is not good or too
incomplete.
HS
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
Hi Dipankar,
Are you expressing the active protease, or the inactive precursor (zymogen)?
Although we never systematically looked at it, I strongly suspect that many
active proteases destroy the expression host and you will therefor only find
clones expressing the protein in inclusion bodies.
Dear Satvik,
An R/Rfree of 0.29/0.35 after one round of automatic model building indicates
that your solution is correct. You can proceed with refinement and rebuilding.
You can take either the monomer-based or dimer-based solution, it does not
matter. Personally I would take the monomer-based
Dear everybody who reacted,
It seems that when the His6 construct crystallizes, there is a fair chance that
the his10 construct will crystallize as well. However, as usual in
crystallography there is no guarantee, so I have added a TEV site to the
construct in order to be able to remove the
Dear Satvik,
You only know if the space group is correct AFTER you solved your structure.
With an Rwork/Rfree of 0.43/0.48, the space group is likely not correct. The
way to solve this is to run MR in all possible space groups. Most, if not all
MR programs have an option to do this
Hi Dave and Tony,
Upon submission, the pdb checks the sequence and automatically generates
comments about sequences derived from the expression vector. So you do not have
to do anything. Given the issues many programs have with non-sequentially
numbered residues, I would also number them
Dear BB,
We are planning the production of a protein for crystallization. From
literature, we know that the construct with a 6-histidine tag crystallizes.
However, for other biophysical measurements, we would prefer to have a
10-histidine tag.
Does anyone has experience with His-6 versus
Dear Cheng,
You could check whether you get irreversible inhibition with your compound,
which could be a sign of a covalent link with the protein.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Savvas
Savvides
Gesendet: Mittwoch, 23. August 2017 21:54
An:
Dear Betty,
You have very high resolution, which helps you to identify your ligand, but the
ligand may be disordered…
What I would do is to place some dummy atoms (e.g. waters) and refine and look
if the molecule gets clearer. By scrolling the density in coot, you can
identify the positions
Hi ???,
I would first try AMPLE, as was suggested by Daniel.
If separate helices still give you an anti-parallel coiled coil, your structure
may in fact be anti-parallel. Your problem is not that the structure has
another parallelity than you would like, but that you cannot solve the MR
Hi ???,
Coiled coil structures can be very tricky with MR, so your solution may not be
correct. You could try to split your search model and run MR with the separate
coils. If you have high enough resolution (> ~2.3 Å?) and your MR solution is
basically correct, you may be able to solve your
Hi Gaoyina,
Maybe a stupid suggestion, but did the paper of the negative stain EM explain
how the complex was prepared? That would be the first thing I would try.
Further, as Abbas explained, the complex may fall apart during gelfiltration.
At least for analytical purposes, you could try to
Hi Chenjun Tang,
From the images you sent, it looks like your crystal suffers from lattice
translocation disorder. See e.g.
http://onlinelibrary.wiley.com/doi/10.1107/S0907444909025153/epdf
Calculating a native Patterson and looking for strange peaks may give some
hints what is going on.
Dear All,
For me this whole discussion is an example of a large number of people barking
at the wrong tree. The real issue is not whether data processing programs print
amongst many quality indicators an Rmerge as well, but the fact that the PDB
and many journals still insist on using the
Dear Megha,
I am puzzled by the results you presented. If you only see the effect in the
presence of your protein, the protein must have something to do with it. The
steep decline points to some highly cooperative effect, which might be
aggregation/precipitation. Did you check that your
Dear Nick,
I would contact some MassSpec people and ask if they could find out the mass of
your mystery ligand. I would also carefully look at the neighboring protein. It
might be an alternate conformation of a partially disordered loop. Finally, I
would check literature to see if a natural
Hi Vincent,
To calculate the best possible (self)rotation function, you want to have as
many as possible intramolecular vectors (within the search molecule) and as
little as possible intramolecular vectors (between molecules in the crystal).
These latter vectors are meaningless (noise) as long
Hi Vipul,
The first thing to do is to check whether the fit of the offending residues in
the electron density maps is correct. If it is not, you have to do rebuilding.
If the fit is correct, I would leave them as they are. Assuming the
distribution of bond lengths and angles has a bell-shape,
Dear Vipul,
the first thing I would check is why one chain has good and the other chain has
poor side chain density. Are the B-factors of one chain much higher than of the
other? Does one chain have more/better crystal contacts to stabilize its
position in the crystal? Is the structure
Hi Roger,
First, sigma is a relative measure. If sigma is very low, e.g. since your map
contains 80% solvent, 3 sigma may correspond to the same absolute value e.g. in
electrons/Å3 as 1 sigma in a standard map, so I would not be worried about that.
However, an Rfree of 0.45 and a large
Dear Vipul,
At this resolution and with these Rfactors you are not supposed to „correct“
the NCS outliers. Look into the electron density maps if they are well defined
and if the different conformations can be explained by e.g. crystal contacts.
However, if they are in a less well-defined
Dear Sutapa,
I fully agree with Grant, the first question is whether the naturally-produced
protein is soluble and whether your protein is not a membrane protein, or a
domain, cut out of a much larger protein? The other question is whether your
protein is toxic for E.coli and only the bacteria
Dear Madhurima,
Small protein structures can be very difficult to solve by MR due to an
unfavorable ratio between inter- and intra-molecular vectors in the pattersons.
I am currently also struggling with some data sets myself.
However, there are things you could (and should) try:
1) If
Dear Petr,
Another possibility is that your very good substrate got turned over by the
enzyme and that the 5 atoms with good electron density you see is all that is
left. When you know the enzymatic reaction, this is easy to check. If this is
the case, you should try a short soak (5-30
Dear Sharifah,
Was no protease inhibitor used during crystallization, or during the whole
purification process? E.g. when a protease inhibitor cocktail was added during
cell-lysis, a protease inhibitor may irreversibly have modified your serine.
If your protein is a protease, it may have
Dear Eleanor,
I did not check the pdb file you mentioned, but I have had a case like that.
The protein formed a complex of 8 large and 8 small subunits with internal 422
symmetry. There was a disulfide link across the internal twofolds and in one of
the crystal forms we got, this internal
Dear Pooja,
A few remarks:
-Matthews does not show 4 chains in the asymmetric unit, it suggests 4
chains. However, in reality it can be more or less chains, although rare, 75%
solvent (2 chains) is not unheard of.
-An initial Rfree of 38% is ok, 32% after refinement is a bit
Yes, Arg has 3 potential Hbond donor/acceptors and Glu 2. Also a single atom
can have multiple interactions.
Look in coot at the structures and which atom has which interaction with which
partner atom.
Best,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board
Dear Smith,
I think your question was clear, and the answer you got was clear as well.
However, I think the question you asked was not the right question. You want to
use a particular phrase to describe your crystal packing and you want the
CCP4BB to endorse this. When the answer was negative,
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