Hard to say without seeing the maps and experimenting. My first check would
be to set the NTD occupancies to 0.0 - refine the CTD alone, then look at
the maps in COOT.
Or maybe let an automatic modelling building program such as Buccaneer try
to rebuild the NTD section, with starting phases from
The traditional benefit was in reducing absorbtion errors. This obviously
depends on crystal path, and seeing it is hard to model well, one way to
mitigate the errors was to average equivalents collected at different
settings. The error was still there, but assuming random distribution about
the
I would think a Google search would make some suggestions for you. There
are lots of cases of proteins which require Calcium to function, but it is
a bit chicken-and-egg-y - can the protein only function after it folds
correctly, and is the Ca essential for that folding?
On 31 May 2013 11:54,
I don't really understand what your space group is? space group mC???
Eleanor
On 10 Jun 2013, at 19:57, Wei Shi wrote:
Hi all,
I was trying to solve the structure of a protein in several different
datasets using xds and phenix. I could solve the structure from one dataset
in space group
If you are resetting B factors you must recalculate the AniosUs later
But if you are getting negative B values something in your procedure is
less than optimal!
Are you refining aniso Us with too limited data? You need high resolution
data to attempt this.
Are you trying to refine B factors and
As others say - the Rfactors look pretty good for MR, mine usually start
over 50% even with a better model and one hopes they then decrease..
But you say you took the Balbes model into phaser? and I think Balbes
automatically runs cycles of refinement so any comment on R factors may not
mean much.
At your resolution that seems to me a reasonable gap between R and Rfree?
Eleanor
On 21 Jun 2013, at 12:28, herman.schreu...@sanofi.com wrote:
Dear Bulletin Board,
After some headbanging (Refmac5 had helpfully created gap records for all
insertions and deletions present in the structure),
You have obviously solved this problem, but one thing that can change
apparent Rfactors is the number of reflections accepted..
If one gives you 5% more very weak reflections say, then those will
inevitably have high Rfactors and this can increase the apparent Rfactor
without changing the map
With that translational vector the data set is approximately I centred.
If you integrate it in I centred lattice then you must consider space
groups I 4 or I41.
In point P4 you might need to consider SGs P4, P41, P42, P43
Eleanor
On 1 July 2013 11:19, rajakumara eerappa reera...@gmail.com
Well - translation peaks are listed in the data processing log file - look for
the word translation. If there is an off-origin peak 25% of the origin you
probably have two 9or more) molecules in similar orientations but displaced
from each other.
Self rotation peaks are listed in various
You are desribing the reason many people limit their refinement to lower
resolution! I think it is probably universally true that there are multiple
conformations for sidechain/water networks at the surface, which we just
dont model properly. If you are going to tackle the fine details you need
Hard to comment without more information, but check how many molecules you
expect per asymmetric unit. If more than one look at the self rotation
function - it might help.
And you can with difficulty do a cross rotation between two data sets,
which sometimes suggests how crystal 1 is related to
I check ha sites by 1) looking at the shelxe plots ( these are displayed in
the CCP4 GUI task - prob also in phenix? )
If there is good contrast for one hand rather than the other the sites are
likely to be correct - if not - hmmm; there might be a reason but they
could be wrong..
Then I check
Oh dear - you should always start refinement against the original processed
data - but others have told you that already..
The TLS files will not be appropriate for the rescaled FPs - it is
surprising that the Rfactor actually goes down though!
Or are you doing several cycles of refinement in
] on behalf of Eleanor
Dodson [eleanor.dod...@york.ac.uk]
*Sent:* Wednesday, July 17, 2013 6:05 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] TLS refinement refmac
Oh dear - you should always start refinement against the original
processed data - but others have told you that already
This is a bit puzzling.
Sticking to point groups:
P3 P6 are sub groups of P6/mmm so data which merges in P6/mmm will
always satisfy P3 and P6.
And twinning in P3 or P6 will make the data seem to have higher symmetry.
Four way twinning is unusual, but possible of course.
But if you really have
that doesnt seem too bad an Rfactor to me! What do you expect?
Eleanor
On 27 August 2013 09:59, Afshan Begum afshan...@yahoo.com wrote:
Hi ccp4 experts,
I have collected diffraction images to 0.96 Angstrom resolution to the edge
of the detector. One data set give me the full completeness
What has happened to the CCP4 update procedure? Shouldnt this mean
latest versions are on that web site?
e
On 4 September 2013 22:57, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk wrote:
Hi
refine bref bonly
should be what you are looking for. You may need to use the latest available
version
First - you probably have the best solution you can hope for - Rs of
27% 33% are not great, but unlikely if you had a wrong answer.
A query though: t is surprising to have a pseudo translation if you
expect one molecule in the asymmetry unit .. an you elborate a bit on
that?
Is there a good
It seems you cannot read either your data or a scratch mtz file - the
log file should tell you its name.
There is obviously something funny - see the discussion of free r reflections..
You dont say your pointgroup - presumably P/mmm or P3m or P6/mmm -
they have that twin law.
But with perfect
This is amazing - I am so glad the Nobel committee has recognised this
ground breaking, rather unglamorous work requiring great intelligence,
very hard work, and a lot of disappointments!
Congratulations to them all, and to the whole field.
Eleanor Dodson
On 10 October 2013 09:26, Alexandre
, otherwise it is straightforward to generate a map
yourself and look at it in coot.
Eleanor Dodson
On 21 October 2013 13:53, Antony Oliver antony.oli...@sussex.ac.uk wrote:
Dear Mahesh,
Are all the structures at similar resolution? Definition of secondary
structure is, and can be, affected
I dont know about LLG scores - they seem extremely variable depending
on the degree of sequence similarity you assign.
However when you get an R/Rfree of 40%/47% that is a pretty good sign
that at least something is correct.
It isnt clear whether that is after you have placed 2 copies of the
reproducible regardless of
the assigned sequence identity.
Best wishes,
Randy
On 21 Oct 2013, at 14:42, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:
I dont know about LLG scores - they seem extremely variable depending
on the degree of sequence similarity you assign.
However when you get an R
Well I would start by flipping the carbonyl oxygen then see if the
side chain can use the density - what are the B values for the
neighbouring stuff?
Eleanor
On 25 October 2013 19:00, Patel, Joe joe.pa...@astrazeneca.com wrote:
Is that a glycine in the sequence next to the Glu/Gln? Have you
There are errors in every branch of human endeavour I am sure!
Please if you find something wrong. send your suggested correction to
Garib Paul, and once there is a fix notify us all via the BB.
CCP4 has always depended heavily on the users noticing the bugs
Thank you for your observation.
Well - years ago I wrote a program called watertidy to do just this -
but it asigned waters as OH0 OH1 OH2 with a according to what atom it
was H bonded too, and those names are not now permitted..
My way now is to read in a completed homologous structure - use SSM to
fit it over the new one -
one in their book, i am sure.
eleanor
On 30 Oct 2013, at 16:05, Gerard Bricogne wrote:
Dear all,
Apologies for such a retro and non-biological question, but would
anyone have a photograph of an Arndt-Wonacott rotation camera that he/she
would be willing to share? I collected data on
What does a straight difference map look like? i.e. omit one nucleotide at a
time, do a few cycles of refinement and then inspect the weighted difference
map - SA may be too violent for your structure.
Eleanor
On 4 Nov 2013, at 06:36, dengzq1987 wrote:
Dear all,
Recently, I received the
It is easy enough if you still ant to do it.
I would feed both into f2mtz separately to make a mysadIplus.mtz and a
mysadImin.mtz
then use CAD to combine and change the default labels to something like I(+)
SIGI(+) and I(-) SIGI(-)
But as George says Why do you want it? That will change the
There are ways - the EM map is your model equiv to a PDB file and you
need to generate a set of structure factors from your map - the EM
density is put into a large box and transformed by a program such as
sfall. .
Is that possible for you? There are problems of scaling etc etc..
On 15
First Q - how good is your data - is there no possibility of twinning
or any other distraction?
Second Q - To compare those results properly we need to know how the
P2 and the P222 cell align - are the cell dimensions more or less the
same?
But the 2 plots you attach (and the list above) show
I guess you have checked that P43212 is a better match than P41212?
(And that you are running REFMAC against an mtz file with the same
symmetry as the input PDB - you may need to change the SG in the mtz
header by hand.
mtzutils hklin P41212.mtz hklout P43212.mtz
symm P43212
end
Or vice versa..
Hmm - why should a translational peak not be along the 40 axis?
Anyway othercell shows this
Conversion of cell 40, 32, 101, 90, 101, 90
can give
Laue groups
C m m m 40.0 198.3 32.0 90.0 90.0 89.60.42 [h,h+2l,-k]
Possible spacegroups:
C 2 2 21
C 2 2 2
or
C 1 2/m 1 40.0
of mtz file and running
refmac for the same PDB input. P43212 is a better match than P41212.
Sincerely,
Dan
From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK on behalf of Eleanor Dodson
eleanor.dod...@york.ac.uk
Sent: Monday, November 18, 2013 8:47 PM
If you suspect your MR solution is crystallographically correct but it
does not represent the biological entity - eg - you will generate a
dimer if you move molecule B by a symmetry operator such -x,y-1/2,1-z
then the easy way is to submit the coordinates to PISA - either in the
CCP4 GUI or send
Well - your R values will probably appear higher than normal - there
will be zones where all reflections are weak..
but the maximum likelihood targets are meant to deal with this reasonably well.
It seems to work and the maps usually look OK! Eleanor
On 25 November 2013 22:31, Niu Tou
Things to check - number of molecules to search for.
You can use Matthewscoeff to get a suggestion - MOLREP does it
autromatically .
Space group - has Phaser chosen as best SG an alternative to that in your
header?
Eleanor
On 16 December 2013 11:03, herman.schreu...@sanofi.com wrote:
Looks
I would find the sites from the PHIC - you need to use CAD to add
Fcalc PHIC and FOM to the original data with Fnative Fderiv DANOderiv
etc
I usually then use SCALEIT to scale native and derivative to Fcalc -
then you know you are roughly on an absolute scale
Then feed those sites into Phaser_EP
Yes - mlphare did, but so does Phaser_ep
E
On 16 December 2013 18:46, Bosch, Juergen jubo...@jhsph.edu wrote:
Didn't mlphare use to print those values in the log file ?
Jürgen
On Dec 15, 2013, at 4:29 PM, David Schuller dj...@cornell.edu wrote:
I have some SIRAS data of a known structure. I
SFCHECK is a very quick and dirty report generator -
On 15 January 2014 21:42, Pavel Afonine pafon...@gmail.com wrote:
Hi Ursula,
you will find answers here:
http://www.phenix-online.org/papers/he5476_reprint.pdf
Pavel
On Wed, Jan 15, 2014 at 1:38 PM, Ursula Schulze-Gahmen
You dont say whether the unit cells are the same?
In cases like this I sbmit both sets of coordinates to PISA - to get the
preferred biological unit and check whether each structure has similar
contacts.
PISA is distributed with CCP4 but the version at the EBI pdb gives prettier
results!
Dont forget that with twinning in apparent point group PG6/mmm the
true SG may be P6i or P3i21
See the twinning notes: http://www.ccp4.ac.uk/dist/html/twinning.html
Detecting twinning can be problematic -
My rule of thumb, following the procedure od ctruncate::
0) Check the matthews
diffracted to some extent. Examples
are: 2tci 3mth 1mpj
Eleanor Dodson
On 30 January 2014 11:06, Bernhard Rupp hofkristall...@gmail.com wrote:
There is one additional point perhaps worth making: As already noted in the
thread, if you have a NCS homo-oligomer, the different copies in general
I am afraid there is no real solution except to read the paper!
And even that doesnt help if you suspect the merging..
There is lots of discussion about the merit of depositing UNMERGED
data - and that would certainly help developers. Add your voice to the
request!
Eleanor
On 30 January 2014
Well - that depends on many things.
Are you sure of the spacegroup? Those R factors sometimes indicate a
wrong selection of SG P212121 instead of P21212 for example..
Are you sure the data is not twinned?
Do the maps show features which are not in the model?
etc etc
Eleanor
On 4 February 2014
:41 AM, Eleanor Dodson eleanor.dod...@york.ac.uk
wrote:
I agree with Frank - it keeps crystallographers modest to know how
challenging wet lab stuff still is..
Eleanor
On 12 February 2014 19:23, Robbie Joosten robbie_joos...@hotmail.com
wrote:
It's not an e-mail bulletin board
The very best advice is: get better data if at all possible. Things
are much easier and more informative at 3A than at 4.2A and even
better at 2.5A.
There are various tricks which might help improve diffraction..
But if you are stuck then:
The partial MR phases are very useful for checking your
One way is this:
Align Domain1 of structure1 to Domain1 of structure 2 on domain 1 (using LSQKAB
or whatever.)
Then align domain2 of the output aligned structure 1 to domain 2 of structure 2
The polar Chi or Kappa or whatever output from that alignment is the angular
shift required
Eleanor
The Best column gives Wilson plot values obtained according to this
reference:
From the Arp/Warp page:
We have implemented an expected Wilson plot derived by Popov
Bourenkov (2003)
On 26 February 2014 10:04, Tao Zhang zhang...@cryst.iphy.ac.cn wrote:
Dear All,
Recently, I have used
I think it may well be a problem with the scaling.
It is hard to get a reasonable estimate of the Wilson B at 3A -
especially in a small cell.
Look at the Log Graph plots - one associated with R factor gives you
Fobs and Fcalc v resolution. They SHOULD overlap pretty well, but
sometimes they dont
There are lots of GLUCOSE type lib files for different sugars.
One way to find what is available is:
From the REfinement GUI click Monomer library sketcher
You get a window with File in the top LH corner
Click on that and ask for Read monomer from library
Then enter a key word GLUCOSE and you
a different protein that
my friend used and refinement Refmac5 worked out.
However I need to add the LINK Command in PDB so CCP4 recognizes that
glucoses connected.
Can I get help please?
Thank you,
Remie
On Mar 5, 2014, at 10:49 AM, Eleanor Dodson eleanor.dod...@york.ac.uk
wrote
You dont say what resolution you are working at, or what the current R
factor is. or how complete the model is.
There are assumptions made in the refinement scaling algorithms and in
their treatment of supposedly poorly ordered solvent which can generate
false density (both positive and
Sorry - hadnt finished..
The twinning tests are distorted by NC translation - usually the L test is
safe, but the others are all suspect..
On 11 March 2014 14:09, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:
What is the NC translation? If there is a factor of 0.5 that makes SG
CB2 0XY, U.K.
www-structmed.cimr.cam.ac.uk
On 11 Mar 2014, at 14:10, Eleanor Dodson eleanor.dod...@york.ac.uk
wrote:
Sorry - hadnt finished..
The twinning tests are distorted by NC translation - usually the L test
is safe, but the others are all suspect..
On 11 March 2014 14
If the twin law is k,h,-l, then your a axis must almost equal the b axis?
And if the twin fraction is 0.48 then you have additional symmetry I guess?
How sure are you that the point group is P4/mmm?
On 13 March 2014 20:41, Teresa Swanson teresa.m.swan...@gmail.com wrote:
Dear collegues,
I think you have solved it! That is an excellent LLG and if you can't see
anything else in the map, then there s prob. not another molecule.
Does it refine? If you look at the maps following refinement any missing
features should become more obvious.
Solvent content of 65% is not uncommon.
a synchrotron trip next week, hopefully this
should help clear things up a bit.
On Wed, Mar 19, 2014 at 12:17 AM, Eleanor Dodson
eleanor.dod...@york.ac.uk wrote:
I think you have solved it! That is an excellent LLG and if you can't
see anything else in the map, then there s prob. not another molecule
This is a problem for the ccp4 team at STFC.
Eleanor
On 20 March 2014 12:11, Ming Sun ms4...@columbia.edu wrote:
Hi All
I'm running molrep on a large complex, while I have met the following two
problems
1) If the pdb model is smaller than the map, is it possible that molrep
could not
You don't say how you are doing the transformation?
I would simply input the file to cad
cad hklin1 thisfile.mtz hklout newfile.mtz
labi file 1 allin
end
I think (and hope) that the data and phases will be converted correctly to the
CCP4 asymmetric unit.
Eleanor
On 25 Mar 2014, at 09:16,
Why dont you try CCP4MG ?
Eleanor
On 22 April 2014 22:37, Xiaoming Ren xiaomingre...@gmail.com wrote:
Dear all:
I am facing a display issue in pymol. In my structure, there is a nucleic
acid chain with some monomers which are modified nucleotides built in
scketcher of ccp4 suite. However,
A technecality - the Dano only contains information about anomalous
scatterers and should therefore show these more precisely.
The 2Fo-Fc map will tend to show anything which is included in the phasing
at the position given.
For safety you can set all the atom occupancies in the vicinity of the
PLEASE do NOT do MR - You will most likely finish up with a different
origin for your SG, and it will make comparisons a pain in the neck!
Just do a rigid body refinement starting with the native structure. If you
like you can change the cell to the substrate one
pdbset xyzin native.pdb xyzout
Look at the aimless plot of CCanom . That is the best indicator I think and
very sensitive when you have such high redundancy
Eleanor
On 25 Apr 2014, at 22:13, Jim Pflugrath wrote:
d/sig should be above 0.80
There seems to be plenty of signal there with all values above 1.02. We have
We need more information.
First if the pointgroup is hexagonal are you searching al likely SPACEgroup
- eg PG P6, SGs might P6 P61 P62P63 P64 P65..
There is a GUI option to do this for both MOLREP Phaser.
You can guess the likely no of molecules using matthews
In the GUI - that is in the MOL
Well - this is pretty common, and really doesnt matter.
I just let SHELXC/D give an occupancy to its anom scatterer solutions
and assume that the stronger one is Ca. But in fact it wont matter at all
for the phasing, and IF the experiment works it is easy to sort out S from
Ca in the final map.
I should be sending thids to the phaser team I guess, but maybe there is an
easy fix..
This is the end of the log file..
Sg I222 or I212121
Scoring 500 randomly sampled orientations and translations
Spreading calculation onto 2 threads.
Generating Statistics for TF SET #1 of 2
0%
This is fixed now if you re-install updates and
Armando - this is crude but if you edit the log file and replace
Rfactor v. resln :N:1,6,7 11 12with Rfactor v. resln :N:1,6,7,11,12
it will work.
On 21 May 2014 10:20, Armando Albert xalb...@iqfr.csic.es wrote:
Dear all,
does anyone
An obvious point - remember refinement exists to give you the best possible
model so you need to look at the maps.
And I guess that has to be a subjective assessment - if you SEE anything
more clearly at the higher resolution - I would use that data, but if the
maps do not improve discard it..
.
In the short term we simply took the processed mtz file and ran
mtzutils hklin1 corrupted.mtz hklout fixed.mtz
SYMM 3018 (or symm P2 21 21 )
and the fixed file was OK
Eleanor Dodson
Do check for any differences in format..
Or attach the sca file and I can check why/what (maybe!)
Eleanor
On 25 May 2014 13:02, chen chenc...@gmail.com wrote:
hi all,
I have an .sca file processed by HKL2000 about 4 years ago, I just used
the Scalepack2mtz program to change it into .mtz
There are differences between the LINK pdb definition and that in REFMAC -
hence the different name LINK and LINKR
LINKR allows you to do this: ie cross reference to a dictionary link which
is much more informative than a simple LINK record which can only define a
link distance.
However for
Can you send more details? the log file? the pdb
On 30 May 2014 22:54, Carter, Charlie car...@med.unc.edu wrote:
This is a bizarre problem. I'm trying to superimpose multiple
conformations of the same protein using segments I expect not to change.
LSQKAB bails with this error each time:
I have seen similar features fairly often when the data collection has been
pushed to the limit.
The theory is that it is due to radiation damage - you could check by only
merging say the first 50% of your data, then seeing if the di-sulphide is
intact in those maps. ( wouldnt re-refine much -
I thought the addition of ... around file names got round this problem
eg
This_is_Mine.pdb and That is Yours.pdb
Eleanor
On 3 June 2014 13:15, Eugene Krissinel eugene.krissi...@stfc.ac.uk wrote:
I am afraid that it is us who will need to conform eventually :), same to
say about Program
It helps to look at the output from the truncate step quite critically.
First is there a non cryst translation of 1/2,1/2,1/2 indicated in the P4
2i2 data set?
If so then the I centring at lower resolution might just be approximate..
If there is NC translation then other twinning statistics are
the problem.
As one suggested offboard (tongue-in-cheek): Why not find crystals that
are not twinned, probably with higher resolution?
I will do that, and thanks again for your input!
All the best,
-Bjørn
On 06/04/2014 03:09 AM, Eleanor Dodson wrote:
It helps to look at the output from
That is puzzling.
18% solvent is not common and you would expect very strong diffraction with
such a low solvent content.
one possibility is that the NC symmetry is parallel to a crystal axis and
is making monoclinic data appear to have an extra 2-fold axis. (There is a
case I have heard of
It is very hard to diagnose this sort of error - I didnt think
scalepack2mtz cared about data quality!
There is more likely some format problem.. Is a sca file meant to have some
sort of terminator?
But best to attach the offending sca file so that experts can check it..
Eleanor
On 26 June 2014
Keep on using the master file.
Refmac corrects the observations in a few ways
The overall anisotropic B correction is always applied
In the worst case scenario where you are refining considering twinning the
2FP2 output is no longer the observed FP but one after a detwinning
correction..
So
It is difficult! Ni Zn are rather interchangable..
You dont say what resolution you have: There will be a small difference in
the number of electrons you expect to see at the metal site, depending on
whether it is Zn Zn2+ etc etc, and you can correct that to take account of
the f' as well.
So
To answer the original question.
The indicators are that it is not twinned,
If the Mean s are close to the untwinned values - you can probably believe
it.
Why are you worried?
Eleanor
Determining possible twin laws.
0 merohedral twin operators found
0 pseudo-merohedral twin operators found
:49 AM, Eleanor Dodson eleanor.dod...@york.ac.uk
wrote:
To answer the original question.
The indicators are that it is not twinned,
If the Mean s are close to the untwinned values - you can probably
believe it.
Why are you worried?
Eleanor
Determining possible twin laws.
0 merohedral
I suggest submitting your coordinates to the PDBe (EBI) web site to run
PISA or using it via tthe CCP4I interface.
This analysing contacts, and suggests the most favoured packing. It is not
fool proof but worth checking.
Eleanor
On 15 July 2014 09:53, herman.schreu...@sanofi.com wrote:
Dear
No need to reindex - just do this to change the space group in the scala
header.
mtzutils hklin1 scala.mtz hklout scala-P22121.mtz
symm P22121
end
There are other ways of course..
Eleanor
On 16 July 2014 13:28, Vajdos, Felix felix.vaj...@pfizer.com wrote:
Dear Sudipta—
Herman is
Yes - is it rot mat? at home so can't check but look at the documentation - I
remember it turned any rotation definition into all the other likely ones…
Eleanor
On 21 Jul 2014, at 05:01, vijay srivastava wrote:
Dear All,
Is there is any program to convert euler angles into theta, phi and
Well yes, The bulk solvent model can distort the density, especially if the
ligand is large.
But it usually isnt too serious - try doing SIMPLE scaling and see if
that has any effect on the appearance of the density
Eleanor
On 22 July 2014 10:16, herman.schreu...@sanofi.com wrote:
Dear
.
http://journals.iucr.org/d/issues/2004/12/01/ba5056/ba5056.pdf (Open
Access)
HTH,
Paul.
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
.html
).Can this also happen with oxygen atoms? What would be an appropriate
way to deal with this issue during refinement? Suggestions greatly
appreciated. Thanks,Chris
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44
was p312 which i obtained by
running a self-rotation function in MOLREP. When i scale my data using p312
spacegroup the chi2 and rejections were huge. But he data was scaling well
in p321 spacegroup. can anyone explain whats going on?
Thank you very much
Deepthi
--
Professor Eleanor Dodson
YSNL
)
***
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
I think the community should thank you Wolfram for all you have contributed
- I do hope this message catches you or someone passes it on!
All the best for your retirement
eleanor Dodson
On 11 April 2012 11:21, Wolfram Saenger saen...@chemie.fu-berlin.de wrote:
Dear CCP4 bulletin board
Cad will do this correctly
Reflection utilitied - merge mtz ( rather confusing job title - sorry..)
mtz in - the P4121.mtz data
Output - P41212-ext.mtz
Defne mtz output
Select define limit for refl;action by Laue code select P1
then you will get a list of all P1 reflections with phases
are they listed (they're not in symop.lib or syminfo.lib)? Or are
they doing some clever projections of the space groups?
Cheers
-- Ian
On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:
Cad will do this correctly
Reflection utilitied - merge mtz ( rather confusing job
Edit, or use coot to reorder chains
If you read that edited pdb into pdbset
pdbset xyzin edited.pdb xyzout edited-and-renumbered.pdb
end
I think the renumbering happens automatically..
Eleanor
On 14 April 2012 09:46, Bernhard Lechtenberg bc...@cam.ac.uk wrote:
In Coot you can use
And Marjorie Hardings results are nicely tabulated on a web site..
Google for it
Eleanor
On 13 April 2012 22:08, Marc Kvansakul m.kvansa...@latrobe.edu.au wrote:
Hi Andre,
Majorie Harding wrote a few nice papers on metal ion binding sites and
their associated coordination geometry,
Nothing profound to add to this interesting discussion, but I too would
like to plug
FobsA - FobsB type maps - when A and B are similar but not quite the same..
It is prudent to omit the interesting parts of model A (or B) - whichever
you use to calculate the PHIC and FOM -
but the peaks and
A jolly good thing - congratulations and thanks to the instigators...
Eleanor
On 13 April 2012 15:40, Gerard DVD Kleywegt ger...@xray.bmc.uu.se wrote:
Hi Paul,
You saw the wwPDB/CCDC JPG in my PPT at GSK :-)
Yes, wwPDB and CCDC have signed an MoU. In pounds and pennies it means,
amongst a
Oh dear - this is the version of Refmac in the latest ccp4 release - can
this be updated on the web site as soon as possible ?
Eleanor
On 16 April 2012 12:02, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk wrote:
Dear Allister
Could you please update refmac version. In the version you it seems
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