Well - I usually work in confunction with the graphics, so you can look
at the regions which differ.
I start with the rms difference. If that is > 2, I think there are
significant changes. So then you have to decide what Q you are asking,
and why. Is it that you want to use a model for Molecul
Yes - that is true.
Any crystal might be split, and give diffraction with overlapping
lattices- ie show non-merohedral twinning. If you are lucky/careful you
might only get a few spots which overlap after integration of one of the
lattices- not enough to be detected as "twinning" from the stat
That translation is interesting - R3 indexed as hexagonal has a
crystallographic translation of 0.667 0.333 0.333, so this one
indicated by SFCHECK is related.
The twinning is not very severe so it should refine OK from the PHASER
solution.
Is that so?
Eleanor
On 04/08/2011 05:50 AM, ka
On 04/08/2011 12:17 PM, krishan wrote:
Dear CCP4BB members,
We are using a script written in python to generate symmetry mates for a
given pdb file using PYMOL. After generating symmetry mates we want to
combine all the symmetry molecules in a single PDB file with all the chains
having uniqu
On 04/08/2011 05:19 PM, Cale Dakwar wrote:
Hello all,
Given a PDB file of a newly solved protein structure, what is the standard
procedure for assigning regions of secondary structure? And by this I mean
to ask, how does one decide which residues form beta strands, which alpha
helices, and so o
On 04/13/2011 09:18 PM, REX PALMER wrote:
Dear All
What is the best program to use for comparing two protein structures which are
very similar both structurally and wrt aa sequence? ie to get the rms
deviations both generally and in selected regions.
Rex Palmer
Birkbeck College
Using CCP4 g
Hmm - I use this quite a bit.
ifier.
You cant start Autoamore for a particular model until that has been
entered into the model database - the first Q you are asked from the GUI
is "Which model?" But you can certainly close the model database once
you have entered the model name with a unique
I dont know - it works for me..
That is under Fedora x
Eleanor
mtz2various HKLIN "./ins_pig_zn_T2_hex-unique_refmac1.mtz" HKLOUT
"./ins_pig_zn_T2_hex-unique_refmac1.hkl"
OUTPUT CNS
labin FP=FP SIGFP=SDFP PHIB=PHIC FREE=FreeR_flag
end
On 04/27/2011 07:26 PM, Kelly Daughtry wrote:
Yes,
I guess one way would be to seperate coordinates..
But doesnt overlapmap do that by default?
Eleanor
On 04/21/2011 10:25 PM, Maher Alayyoubi wrote:
Hi Everybody, I posted a question earlier on the bulletin regarding
how to calculate the map correlation coefficient using Overlapamp or
any othe
This may be too late to be of use, but as one of the authors of the
sfall/overlapmap system..
sfall does generate a coded map which flags every grid point with a
unique ID of the nearest atom, ie one which is unique providing there
are not too many atoms - it is adequate for most molecules tho
On 05/11/2011 10:30 AM, ka...@ssl.serc.iisc.ernet.in wrote:
Dear users,
I have refined a structure in R3 with cadmium bound to it, which
was present in the crystallization condition. There are 2 chains
in the asu. The structure is twinned. R and Rfree is around 22% and
28%. One of the cadmiu
On 05/12/2011 08:13 PM, Fulvio Saccoccia wrote:
Dear ccp4 users,
I need to generate intensities from a model (.pdb). That is, I think that a
correct procedure could be to convert model to structure factor and then obtain
intensities squaring the SF.
Does anyone know how can I do?
Thanks in advan
If you have model coordinates for your CSA, I send those to the PRODRG
server and let it generate a REFMAC style dictionary.
You will need to make sure it is labelled as a peptide - cf the standatd
residue cif files to see how to do that..
Then you need to enter the LINKR record into the pdb fi
I dont think there is an Rfree problem..
At 2.7A you expect quite a big difference between R and Rfree
Reducing the resolution will a) probably makethe Rfree/R difference
greater, and b) degrade the quality of your maps and model.
Eleanor
On 05/21/2011 02:28 AM, Seema Mittal wrote:
Hi Ethan,
The default output for REFMAC
Missing Data: For those reflections where the FP are missing, mFo is set
equal to dFc. Hence the terms become FWT=dFC and DELFWT=0.0.
the Rfree reflections are counted as "missing" hence there shouldnt be
any bias intoroduced towards those Fobs assigned as free
How very odd!
I have no ideas on the Zn phenonema - what do the R factor plots look
like against resolution - is there some aberrant reflection which was
part of the FreeR set? The theory is that excluding 5% of the data
should not affect the model seriously at all..
Re the 2nd point. Two
I havent used maprot for years. COOT does it very quickly and
automatically.
But it is tricky to get the matrices correct - can you give some more
details and I will try to help
Eleanor
On 05/27/2011 11:33 PM, Francis E Reyes wrote:
Hi all
I was just fiddling around with ncs and maps, so I tr
Use the GUI
Just feed the 2 sca files into pointless - choose one as the reference -
it really shouldnt match which..
pointless will check the indexing is consistent, then give you an output
file with the two sets merged and sorted together, with different batch
numbers assigned.
scala wil
On 06/03/2011 02:01 PM, Careina Edgooms wrote:
Dear ccp4 members
I have question about how to interpret polarrfn log. I wish to know if my
crystal display NCS. I am not sure how to interpret the file. I see it have two
peak, one is origin and the other is not that high to me. I have attach copy
I cant comment on the pictures - but to calculate an anom map -
if you have run REFMAC you will need to CAD together the refmac output
plus the Dano & SIGdano in the data processed file
Use reflection utilies
Merge mtz files
then Map utilities
FFT - select anomalous
Fill in columns Dano p
Is the documentation for Matthews coefficient sufficient?
See
http://www.ccp4.ac.uk/dist/html/matthews_coef.html
You obviously need to know what you expect to find in that unit cell..
And before you can work out the volume of a P21 cell you also need to
know the beta angle..
Eleanor
On
Reindex your data as -h -k l or h -k -l - this will automatically
change the cell to berta = 90.4
eleanor
On 06/08/2011 04:10 PM, Vellieux Frederic wrote:
Zhiyi Wei wrote:
Dear all,
I have a P2 derivative dataset with beta=89.6. I try to change the
beta to 90.4 to be consistent with t
On 06/08/2011 07:19 PM, Shiva Bhowmik wrote:
Dear All,
I am working on a protein structure that yielded comparable diffraction
quality crystals from two different crystallization condition. One of the
crystallization condition conatins high conc. of salt pptant whereas the
oher one contains hig
First Q.
Checking the refined structure in detail..
This is personal.
Basic - run REFMAC with monitor many - that lists really bad bonds,
chirality, symmetry clashes etc, but frankly by the time you are at
R=20% there shouldnt be many of those..
You need to be sure you have described any CIS pe
It helps to keep the same water naming convention in all the complexes.
distang is a slow tool but it will list all contacts to a given set of
atomic radii. I use that output a lot to check on interesting contacts..
But in the end it boils down to thoughtful book-keeping..
Eleanor
On 06/14/
It looks like a rhombehedral data set with small deviations from the
exact H3 symmetry to give the weak spots.
The standard H3 setting has origins at (0,0,0) (1/3, 2/3, 2/3) and
(2/3,1/3,1/3) so to get your translation vector to match the
conventional H3 one, you will have to reindex the P321
On 06/24/2011 08:50 AM, mullapudi edukondalu wrote:
Dear Members,
I have my first data set on one of my protein crystals, that diffract to
2.7 A, and the space group is I222. According to Mathews coefficient, there
should be 4 molecules in the asymmetric unit. But, when I run molecular
replacem
Well - it isnt surprising that all your geometry is "good" at the start.
You have fitted a refined structure against a a different crystal form,
so the first geometry report relates to your starting model which will
not be the true model which fits your new data.
Refinement has to push that mo
On 06/29/2011 10:22 PM, Paul Lindblom wrote:
Hi everybody,
can anybody tell me how crystal contacts are defined? Are there good and bad
crystal contacts? They are the most important interactions with impact on
the crystal quality, but they are not of covalent nature, aren´t they?
With best rega
Well - you have a problem of chain IDS,
but pdbset xyzin asymm.pdb xyzout whole-cell.pdb
symgen P212121 (say)
end
will generate a whole unit cell,
then
pdbset xyzin whole-cell.pdb xyzout whole-cell-+100
symgen x+1,y,z
end
etc
will move that unitcell.pdb
You would have to put them all together
Can you send a bit of the input file and the command script generated by
the GUI
Eleanor
On 07/02/2011 07:48 AM, Sudhir Kumar wrote:
Dear all
I am trying to convert a scaled file (scaled using Automar) to mtz butit is
showing follwoing error
:
#CCP4I TERMINATION STATUS 0 Error from script
/o
This is a problem not properly addressed - if you generate your
FreeRflags in the highest possible Laue group for a system - eg P6/mmm
if you SG is trigonal, then add these to the lower symmetry reflection
list you are safe. It really should be done at the pointless stage but
it isnt..
Here i
On 07/04/2011 04:24 PM, ruheng wrote:
>
> Dear all,
>
> Recently we are working on an archaebacteria protein which was expressed and
> purified from E.coli by conventional procedures. After we solved the
> structure, we found that there is an extra density in one of the argninine as
> shown in
There are tools out there that calculate such a map.
REVISE is one - I guess i is in the list of CCP4 programs.
i often do both maps independently and look at them for common peaks
The trouble is that dispersive differences are often less reliable than
the anomalous ones..
Eleanor
07/06/20
If there is no indication of twinning and your Rmerge is sensible then
it is probably point group P222
Run pointless - that gives you the quality of each of the 2 folds sepera
tely..
Deciding on the spacegroup is a bit trickier.
That depends on absences along h00 0k0 and 00l, and if there i
On 07/09/2011 03:49 AM, weifeng wrote:
>
> Dear All,
> There are 8 moleculars in an asymmetry unit, but only one molecular should be
> rebulit, what can I do ?
> Thanks a lot!
> Wei Feng
>
Use coot - average maps over your best molecule, rebuild that - sav
ctruncate style Wilson plot is the old form
log / )
I believe "Wilson plot estimated B factor" is am Arp_Warp style plot
where ) is replaced by a more sophisticated
estimate of expecting scattering. You will have to look at a Arp_warp
publication for details..
Eleanor
On 08/11/2011 07:4
There are 2 rogue reflections in a data set I have here. How can I
eliminate them?
I thought sftools did this but i cant seem to get the syntax right.
Short of dumping the whole file, using an editor, then reconstructing it
I am stuck..
Eleanor
There are many and various programs that do this.
As Martin says - cad will do it - you can use the GUI to change each
data set in the file..
if there is only one data set the easiest is this:
mtzutils hklin old.mtz hklout new.mtz
CELL 168.981 168.981 168.981 90 90 90
end
eleanor
martyn.
,
or refines against the original twinned data like (I believe) phenix and
shelxl.
Thx, BR
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Eleanor Dodson
Sent: Tuesday, August 04, 2009 1:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb
First you must be on the same origin
There are various ways to get there - brute force method is to calculate
phases from both models, combine them, and use the reflection utility
phase match to move one to the other by an appropriate origin shift...
Then
Use the GUI map correlation.
It will
I think you have a found a supercell and dont really need to run any MR
program to find the solution - just reposition the molecule
Your P422 point group cell is
126.514 126.514 76.766 90.00 90.00 90.00
Your I422 point group cellis:
180.096 180.096 152.530 90.00 90.00 90.00
Note c
Hmm - I dont understand that.
I ran structure idealisation on both examples and that tidies up the
geometry perfectly..
Are there some clashes with pre-existing water molecules or other
indicators in the log file that one conformation is suspect?(Look for
warnings..)
Eleanor
John Pasca
One easy suggestion - try buccaneer and refinement!
Eleanor
The Arp/warp people will have to fix this..
Anita Lewit-Bentley wrote:
Dear all,
I have a nice MAD map produced by Sharp and would like to trace a chain
into it using Arp/wArp. When I input the mtz file via the CCP4i
interface, I
Pankaj Chauhan wrote:
Hi all,
In one of my 2.52 A structure, which is dimeric, the R-factor is 21.4 and
free-R is 29.3. I have tried all ways to reduce the free-R including TLS
(even by defining the number of TLS group per chain), but still factors are
not getting reduced. Even i have tried some
Paul will have to answer re 20 NCS operators in coot..
But you dont need to generate the operators yourself.
If you have a master coordinate set with all 20 copies you can use coot
to build one into the average map, then generate all the others by
asking to match chain A to B, A to C etc.. wi
Well - cad cant work with that script so somehow it is being generated
wrongly, presumanly in Arp/warp stage..
It would need input such as:
LABIN FILE 1 E1=FBshasol E2 = something - presumably SIGFBshasol
Eleanor
Narayanan Ramasubbu wrote:
Hi:
Sorry for the same posting in here as well b
The 2nd peak is a shoulder of the origin peak at 1.0 0 0 so should be
ignored..
The 3rd peak is 16% of the origin - rather marginal I would say. So I
dont think there is clear evidence of translational NCS
Eleanor
Sylvia Fanucchi wrote:
Morning all
Apologies for the simple question.
hypFdemo_28.pdb:
CRYST1 58.351 58.351 155.876 90.00 90.00 120.00 R 3 2 :H 1
I dont hold a candle for either of these SGs but Phaser is now
outputting the R 3 2 :H and many many other CCP4 programs are then
falling over
Can the symlib be modified to accept both?
Eleanor
C 2."
-- The RCSB
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html
I don't understand why specifications aren't consulted. It seems a lot
easier to create a record that conforms to the most widely accepted
specification than to invent a parser that can read any format one can
possibly
Just a correction - ccp4 had NOTHING to do with H32 definitions - just
followed the wwwPDB requirements.. there were bitter arguments over
accepting it from many!
E
Peter Zwart wrote:
Hi Stephen,
R32
H32
R32 :H
Correct. These are all hexagonal setting. As far as I know, the
hexagonal set
Jason Porta wrote:
Hi everybody,
I would like to take two mtz files (which are very similar) and calculate
the R-merge between them. I tried looking into CCP4 and Phenix, but could
not find a direct path. Does anybody know how I can do this R-merge calculation?
Best regards,
Jason Porta
If
Can we have more details?
Do you only have 3.6A data? If so it is quite likely there is a good
deal of real disorder? Or that your MR solution was slightly out for
that molecule.. Could you have the wrong soacegroup - one related to the
one you are using?
Are the two heterodimers related by
Well - it certainly SHOULDnt happen! But there seems to be a bug in CAD
I am having trouble testing it but will keep on trying..
Eleanor
wtempel wrote:
Dear colleagues,
trying to be a responsible citizen, I occasionally activate the "Copy
Rfree from another MTZ" button in the {Data Reduction|Im
Too many peaks, all with similar Z scores isnt a very good sign - one
prefers high contrast but it is hard to make a rule - it depends on many
factors; number of molecules in asymmetric unit, similarity of model and
new structure, data quality, etc etc..
The automated procedures, MrBump or Bal
james09 pruza wrote:
Dear All,
I am using Refmac5 and have metal in the structure. The refmac program is
not reading this from the library file and hence not refining this metal
ion.
What is the way to solve this problem.
Thanks in advance.
J...
Do you have the correct format for the ATOM r
The obvious Q is whether there is some additive in the crystallisation
or cryo which could be showing up in the maps..
But in such a high symmetry space group is it possible that the blobs
are on some symmetry axis? I sometimes observe awful holes or peaks on 3
fold axes, where I think any "no
Just to avoid any problem
pdbcur xyzin X.pdb xyzout X-nohyd.pdb
DELHYD
END
Eleanor
Francois Berenger wrote:
Markus Rudolph wrote:
Hello,
long ago I had a case when HG1 etc. were interpreted as mercury by
phaser.
Could that be relevant to your case?
I hope not.
However, as I have alrea
Francis E Reyes wrote:
Hi all
I have data integrated and scaled to P21 via denzo/scalepack. I'm concerned about
the workflow to obtain the alternate indexing arrangement (h,k,l) -> (h,-k,-h-l).
I was thinking .sca ( not specifying NO MERGE) -> .mtz -> reindex but the
documentation for reind
PISA will do that - an EBI service or available less prettily from ccp4i
Eleanot
Miri Hirshberg wrote:
Sun., Jan. 17th 2010
EBI
Greetings,
I am looking for a 3D structure superposition program which takes
two structures and superpose them based only on the coordinates X,Y,Z
regardless of of re
Are you sure you have tested all possible spacegroups?
After data processing you will probably know the point group but any
decision on the spacegroup is dependent on a few systematic absences. If
there is an ambiguity you need to test all spacegroup possibilities..
Eleanor
Muhammed bashir Kh
Ask Kevn Cowtan for his newest csymmatch ( or is it in ccp4.6.3?)
csymmatch -pdbin-ref sol1.pdb -pdbin sol2.pdb
It checks origins as well as moving sol2 to the closest symmetry copy of
sol1.pdb
A brilliant program - should be part of many many pipelines..
Eleanor
Martyn Winn wrote:
refor
There are a good many coiled coil models available. I suggest you search
the pdb for more models yourself, or let a program like BALBES do it for
you and do the MR searches as well.
IF you get a faint hit (usually marked by both R and rfree dropping a
few % on refinement) then Arp-warp or bucc
Those B factors probably mean the atoms are in the wrong place..
eleanor
Sangeetha Vedula wrote:
Dear all,
I am refining a crystal structure with two enantiomers of the ligand lying
on a two-fold crystallographic axis (making the density an average of 4
orientations/optical identity). The liga
Yes - we are puzzling over the same phenomena.
Look at this web site set up by Marjorie Harding
http://tanna.bch.ed.ac.uk/
It lists the likely coordination patterns.
We certainly have ideal Na bonding in our structure - but unfortunately
we wanted to find Ca which has a very similar pattern!!
Two possible points. Could there be a problem with twinning, or
spacegroup? The Rfactors seem rather high..
You dont say whether you have a non-crystallographic translation, but it
is faintly possible with 2 molecules that the SG is actually C222 ..
Or that twinning could be present - look a
I am no expert on CNS files, but do the entries for F_BULK and F_MODEL
correspond to an amplitude and a phase - it certainly looks like that..
If so you can read both in:
I havent checked the format but your script would look like this
title [No title given]
format
'(6X,3F5.0,6X,F10.0,6X,F10.
CCP4 contributer lets keep it as broad based as possible.
Maybe we should subscribe to the PHENIX BB and suggest alternative
solutions there!
Eleanor Dodson
George M. Sheldrick wrote:
I am inclined to agree with Gerard. Of course if there is a specific
question to CCP4bb about SHELX, I try to
I accidently read this page..
http://www.majorgroove.org/questions/93/leu-val-rotamers
It explains a nightmare scenario which has been bugging me for some time
asw I tried to make a beautifully defined VAL fit the density in COOT..
If by some accident your VAL or LEU have the "wrong" naming
would ssm serve your purpose?
eleanor
ebi or ccp4i
Miri Hirshberg wrote:
Sun., Jan. 17th 2010
EBI
Greetings,
I am looking for a 3D structure superposition program which takes
two structures and superpose them based only on the coordinates X,Y,Z
regardless of of residue/atoms name.
(both f
Katarina Moravcevic wrote:
Dear all,
I am refining a structure of a protein in a complex with phosphorylated
ligand (inositol ring). My problem is that after restrained refinement with
Refmac, the ring is distorted in geometrically impossible ways. Could
anybody advise me on how to deal with th
Dirk is right. It isnt so much a GUI bug as a feature!
When you press restart for any job the previous parameters are loaded
into the script.
Usually this saves you work, but if you are changing from TLS with
initial B fixed to 20 to restrained refinement it is undesirable to keep
that fixed
It is common - errors seem to pile up there..
Eleanor
Francis E Reyes wrote:
Is this a cause for concern? FOM's are over 0.5 and Phasing Power is over 2.0.
Thanks
FR
-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pg
Twinning just requires some geometric relation between crystal axes to
yes - it is possible in p1
othercell will tell you if there is some other indexing which will
generate a similar arrangement of axes.
It could be possible that it has higher symmetry of course.
Eleanor
José Trincão wrot
I presume you have a dictionary for both SAM and SAH? You need SAM at
least to use COOT.
My method is to calculate a difference map with the SAM density - xclude
all atoms like SAH or waters which might overlap SAM, then manually grad
the SAM to the right place and run real space refinement
I assume the native and Se-met are isomorphous and indexed on the same
convention?
pOINTLESS will check the indexing convention for you.
Then you must use cad to merge the native and the phased data.
I am not sure of PHENIX output but you need an mtz file with
h k l Fnat etc F-Semet ... PHI FO
The best check for what to expect in an asymmetric unit is to run
matthews. It works out the volume of your asymmetric unit, the volume
your molecule should occupy ( based on mol. wt or number of residues)
and indicates whether you could fit one, two and so on molecules into
the cells asymmetr
I think your crystallographic colleague is misled.
SCALEIT simply scals two or more sets of ampiltudes to the chosen one. (
labelled FPH1 FPH2 etc scaled to FP..)
It knows nothing of the contents of the asymmetric unit..
truncate uses the number of residues in the asymmetric unitr to assign a
Mark J. van Raaij wrote:
apologies for that question - it IS there, two positions about space group search ("X-ray cell
dimensions"). Can't figure out why I did not see this...looking with my ears I guess...
Mark
Doesnt the oca search allow you to set both?
Eleanor
When I deposit at the EBI the deposition software moves solvent to
assocoiate with a protein molecule. If that has been done, those
messages would mean that the solvent is indeed unconnected to anything.
It seems a bit unlikely chemically - and I would check the maps..
has something beem miss
Isnt it in the scala documentation?
Eleanor
Jacob Keller wrote:
Dear Crystallographers,
A basic question: what is the equation currently used to combine/merge
multiple measurements of I and sigI? (Or a reference would be fine as
well (or maybe better.))
Thanks,
Jacob Keller
**
I absolutely agree with Clemens; self rotation functions can mislead in
some cases, and confuse in many more.. A peak in a self rotation does
NOT mean you have a dimer or a trimer - just that one molecule in the
asu can be related to another by the given operator. So for any peak
ther are nsym*
It is quite instructibe to draw the 2-d vector representing the
amplitude and then the error vector when you assume certain things...
Change the magnitude by 50% and see the error vector, then change the
phase by a random shift - say 90 degrees and draw the error vector. In
general it is much mo
Francois Berenger wrote:
Hello,
Is there a ccp4 tool to find automatically the smallest virtual
orthogonal "box" that contain a given PDB ?
Even if your favorite tool is not part of ccp4, I would be happy
to know about it. ;)
Thanks,
Francois.
pdbset xyzin thisprotein.pdb
end
This prints out
Daniel Bonsor wrote:
How do I convert the B-factors from my final structure to full B factors if I did not use TLS refinement? I have been refining isotropic B-factors. Do I switch to overall B-factor refinement, do something else, or have I missed the point altogether?
It may be a dumb questio
Just some ideas. NCS usually good with 2.7A data, TLS only to be used
when model is complete..
You say Matthews suggest 11 molecules, but you only find 6 - doesnt
this mean you have a very high solvent content?
I would check the MR carefully.
How are the 6 molecules related - are there dimer
You need to tell us the spacegroup for us to be very helpful...
And I often find the molrep plots less useful than the list of peaks and
all the symmetry equivalents..
(It has a weird name - *rf or *doc I think)
But I guess all the variant are in point group P222? There are the 3
expected 2
Rex Palmer wrote:
What seems to be a possible sulphate has been identified in our electron
density.
What steps could/should be taken to confirm or consolidate this assignment that
would satisfy referees?
Rex Palmer
Birkbeck College
If you place a sulphate and it refines in a sensible way -
You can feed the SHELX sites into phaser_er or CRANK both of which will
give this sort of information.
Or mlphare if you know how to set it up..
Eleanor
Harmer, Nicholas wrote:
Dear CCP4ers,
I've been asked by a referee to provide the phasing statistics for a SAD
dataset that I used to sol
A thought - are these molecules related by a non-crystallographic
translation involving 0.5 along any axes. In such a case it is easy to
get the space group wrong, and assign a "1 axis when it is really only a
pseudo 21. if that happends your refinement will stick..
I think that at that resolu
I thought truncate applied the scale but not the B value.
you can use CAD to apply a scale
- see the documentattion..
And yo can rerun truncate to check that you now have a fle with B =0, nd
scale = 1..
but why do you want to do that?
All refinement will rescale your output Fs to the model
I know this is a disputed topic, but is there any reference where
anyone has systematically tested different res cut offs for refinement?
Eleanor
..)
Eleanor Dodson
Soisson, Stephen M wrote:
This is an interesting thread, and perhaps I should not dive in on such
a heady topic, BUT, I do want to point out my own particular bias
regarding FOM that is not entirely consistent with James' point of view.
In my experience, the FOM obtained after de
In this lab there are as many takes on this as there are
crystallographers I think! It seems to depend on personality - are you a
wild optimist who traces connectivity at 0.5 Sigma - or a cautious soul
who hates to be wrong..
It seems to me that there are often disordered regions we can never
Wasnt it the tramp whom they beat to death - and the book was R James..
That movie gave the cold shivers..
eleanor
Philip Leonard wrote:
I have a vague recollection of a student carrying books about
crystallography getting beaten up at the start of Clockwork Orange. This
might only be in the b
The newest refmac will deal with this and generate maps with twinning
corrected..
Eleanor
protein.chemist protein.chemist wrote:
Hi All,
I have a dataset that shows about 50 % twinning. I was curious what will be
the best way for the refinement and calculation of electron density maps,
includ
I am a bit out of touch with the discussion, and this may have been
mentioned already.
It is important to remember that Sigma is an OVERALL value for the whole
map, whereas one is looking for local solutions when fitting any
density. Stuff on the surface of the molecule ought to be contoured a
No - no - no!
Probably you should have integrated to a higher resolution!
Eleanor
Daniel Bonsor wrote:
Hello again.
At first I was not worry but maybe now I am. I have completed a structure and
submitted to the PDB. They queried my Rsym value in the highest resolution bin,
2.5-2.37A (may I
A few comments -
you dont give your cell dimensions but if they are more or less the same
for the P212121 and P43 21 2 I dont see how a 43 set of absences can
turn into a 21 set ..
However if there is non-crystallographic translation, then absences an
mislead.. Is that true for you -
Tw
A general point often overlooked, the Rfactor from twinned refinement
at least with SHELX and REFMAC do not use exactly the same formulation
as an Rfactor for a mono-crystal and seems consistently lower than
expected.. my impression is that they cannot be compared easily.
And there may be a pr
301 - 400 of 1650 matches
Mail list logo
