Its more history than science, but for posterity I have started putting
together some images and other memorabilia of the Hilger and Watts
diffractometer, which some may remember!
In case anyone is interested, the link is here:
hilgerwatts.blogspot.com
Feel free to drop me a line if you have an
Hello, it looks as though the No observations that phenix is reporting is
exactly twice the number of unique reflections. Perhaps phenix is reporting the
merging statistics for the Friedel pairs (i.e. F(+) and F(-)) within your
merged dataset. Hence the stats look much better than those for the
Hello, you are right but you can get round it by reading in a cif for D-ala
first i.e. 'Import cif dictionary' before doing the 'Get Monomer' thing. I got
the cif file from the web (its attached). If you do this in the right order you
do get a D-ala on the screen!
On Wednesday, 30 October 2
Hello Eleanor
If I may ask, are you sure the pucker is correct for the proline on the left?
In my humble opinion the proline C-alpha doesn't look very tetrahedral and
maybe this residue has some unexplained density at the back. Maybe the peptide
with the odd extension wants to go down and to th
Hello, I am sure that you have found that if you apply the symmetry operations
yourself, the resulting molecules can come out miles apart, so you need to find
the right unit cell translations that bring them close together again to
generate the real crystal packing. Coot does all this very well
Hello,
Re: "I think you’re asking about 2 proteins with a similar fold having similar
but not exactly the same functions - yes, that does occur."
Indeed, I suspect it is very common, if not the norm. OK, so I now
gather/remember moonlighting proteins are ones with more than one function -
than
I'm probably going to be beaten on this one, as you probably know, it has been
discussed here recently:
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg47716.html
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;d908309.1911
The thing was to re-install Xquartz. I'm not a mac-person
And here:
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg48104.html
Best wishes, Jon Cooper.
On Monday, 9 March 2020, 23:13:15 GMT, Jonathan Cooper
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
I'm probably going to be beaten on this one, as you probably k
A bit off-topic, and not wishing to tempt fate, of course, here are the No.
cases by date for two typical outer-London boroughs (of absolutely no
particular interest to me ;-), one about 4 times bigger than the other:
http://u.cubeupload.com/jbcooper/2020032316h22m13s.png
Could I be forgiven fo
If you can model it as a lysine, it will be the beta-ME adduct. There's a good
one in 1b4e (see attached) which Eileen Jaffe pointed out to me and I never got
round to sorting out. Now there's another one of 'mine' for which the data have
not been deposited, but I did put the images on zenodo 4
Sorry, that was the wrong zenodo link! The correct one is:
https://doi.org/10.5281/zenodo.220983
On Friday, 27 March 2020, 23:06:01 GMT, Jonathan Cooper
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
If you can model it as a lysine, it will be the beta-ME adduct. The
Occupancy.
On Sunday, 26 April 2020, 20:41:49 BST, Abhishek Anan
wrote:
Dear all,
Thanks for the suggestions. It is synthetic peptide so the residue
identity is unambiguous.
I am not clear on how to model both MET and SME in coot, do a real
space refinement and then save the file for
Ian, I can, as a not very scientific footnote, confirm that Jim Austin still
has your Convex on his farm and, it seems, most of the manuals:
http://u.cubeupload.com/jbcooper/smallIMGP0087.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0086.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0078.jpg
ht
I remember we discussed this a lot about a year ago when Ed Berry revived a
thread from 2003!
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind1905&L=CCP4BB&O=D&P=72099
I think the upshot of it all was that you do not need to use shells even with
quite high NCS since Ian Tickle rightly pers
Title: New X-ray Developments and Macromolecular Structures in the Bragg
Centenary Year.
Venue: King’s College London.
Date: 16th December 2013.
Organisers: Dr Yu-Wai Chen and Prof Mark Sanderson.
- - - - - - -
Invited speakers include:
Bonnie Wallace, Birkbeck College London. “Voltage-g
places still available register on the day
BCA Winter Meeting 2013
Title: New X-ray Developments and Macromolecular Structures in the Bragg
Centenary Year.
Venue: King’s College London (New Hunt's House, Guy's Campus, London Bridge,
SE1 1UL).
Date: 16th December 2013.
Organiser
Dear BCA members,
The 2014 Spring BCA meeting is not far away now and the abstract submission
deadline is fast approaching – 1 week remains!
Abstracts can be submitted at:
http://www.hg3.co.uk/bca/
The deadline for submissions is 9 am on Monday January 20th. This deadline
applies to both oral a
Evening all.
It seems that the publisher of my efforts to update the 'Crystals, X-rays and
Proteins' book by Dennis Sherwood would like to print a revised version, so I
was wondering if anyone has noted any typos, glitches, misprints, etc, perhaps
they could possibly let me know, in return for
Hello, on linux (Lubuntu) my install of the latest ccp4i2 does not allow me to
change certain options, e.g. from isotropic to anisotropic refinement:
www.ucl.ac.uk/~rmhajc0/jbc.jpg
whereas my spy with a Mac gets:
www.ucl.ac.uk/~rmhajc0/jg.jpg
and the desired options are there and working.
Any
[SOLVED] Sorry folks, that was an easy one, "Clone Job" sorted it. Thanks for
the tip Huw.
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On Wed, 24 Apr 2019 at 23:14, Huw
Jenkins<288da93ae744-dmarc-requ...@jiscmail.ac.uk> wrote: Hi,
> On 24 Apr 2019, at 22:42, Jonathan Cooper
Hello Tiantian
since there don't seem to be any replies to your message, I can suggest looking
at the following points:
1) What is the unit cell and space group? Is there any scope for misindexing or
twinning problems?
2) You have several heavy atom datasets, so why do you want to solve it with
One thing I have wondered about Coot is when you add new waters into the
structure and these go into a molecule called 'Pointer Atoms...', I have never
worked out how to get the symmetry mates of these newly inserted waters to
appear unless I eventually merge them into the same pdb file as the p
- you can always delete them or change the
occupancy if there is a clash..Eleanor
On Tue, 30 Apr 2019 at 21:21, Jonathan Cooper
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
One thing I have wondered about Coot is when you add new waters into the
structure and these go into a molecule
In the output statistics part of the GUI there is table of mean B-factors, e.g.
Chain mean B (No. atoms) AAA 23.6( 2596 )AaA 35.4( 29 )AbA 35.2( 10 )AcA 18.9(
10 )AdA 58.5( 10 )AeA 39.5( 119 )BBB 25.5( 2545 )BaB 42.0( 10 )BbB 46.9( 5 )BcB
37.3( 92 )
There is an A- and a B-chain in the structure,
The numbers do make sense now: AaA, AbA, etc, correspond to different HETATM
groups and (what was confusing me a lot) the No. atoms includes riding
hydrogens.
On Thursday, 2 May 2019, 23:27:49 BST, Jonathan Cooper
wrote:
In the output statistics part of the GUI there is table of
I am interested in why you want to join 16 mtz files sideways. That is a lot
of derivatives.
On Saturday, 11 May 2019, 20:10:16 BST, CCP4BB
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
That'll teach me to reply straight off a flight from SFO...
Harry--Dr Harry Powell
On 11 M
Having been fond of the idea discussed above i.e. that when NCS is present,
one should have the R-free set chosen in shells, I did some simple tests. Many
others must have done the same, but here's how it went:
1) Choose a few familiar structures, both with and without NCS and get the data.
2) S
When you refine structures with disulphide bridges you often get negative
difference density for the sulphurs, presumably due to the well-known radiation
damage effects. The negative difference density often won't disappear with
usual B-factor refinement. However, it seems to go away if you refi
Re: question 2, for simplicity, I would call it all one helix and regard the
3-10 part as a distortion. Just my opinion.
Sent from Yahoo Mail on Android
On Tue, 28 May 2019 at 13:48, Paul Emsley wrote:
On 28/05/2019 11:51, Stephan Grunwald wrote:
>
> I [have] recently solved [my] first
Hello, can you use the pisa server or similar to compare the extent of
domain-domain and domain-DNA contacts versus crystal contacts in your
structures? It might help to show which is the dominant factor affecting domain
orientation.
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On Tue, 28 May 2019 at 1
Does the SAXS model contain more than one subunit? If so, I would be tempted to
go back to the model and try each one separately. This may not apply, but if
there are monomers in the SAXS model that are related by space group symmetry
in the crystal, I think the MR would never work. Good luck wi
ology 1607, Springer protocols).
I hope this helps to clarify a few issues.
dusan turk
> On 25 May 2019, at 01:00, CCP4BB automatic digest system
> wrote:
>
> Date: Fri, 24 May 2019 22:27:28 +
> From: Jonathan Cooper
> Subject: Re: Does ncs bias R-free? And if so, can
Ian, statistics is not my forte, but I don't think anyone is suggesting that
the measurement errors of NCS-related reflection amplitudes are correlated. In
simple terms, since NCS-related F's should be correlated, the working-set
reflection amplitudes could be correlated with those in the test-
For the past few weeks I have noticed that when you start Coot from the i2 gui
it works fine for up to an hour or so but then its hangs completely and any
unsaved changes go missing. It seems more stable if I start it outside the i2
gui. Is this just me or my linux box?
rting time, rather than using the same
timer for everyone.
Cheers
-- Ian
On Fri, 24 May 2019 at 23:27, Jonathan Cooper
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
Having been fond of the idea discussed above i.e. that when NCS is present,
one should have the R-free set chos
I was wondering why everything appears twice in the report, as below ;-?
https://www.ucl.ac.uk/~rmhajc0/percycle.jpg
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin
In the Phenix reflection file editor, where you pick the R-free set, there are
two boxes where you can enter the fraction of reflections to go into the test
set (see below), but they don't seem to talk to each other. Change the one in
the "More options" sub-menu and the other stays the same with
> >> between the test-set and the working-set F's due to NCS would be expected
> >> to reduce R-free". If the working and test sets are correlated by NCS that
> >> would mean that Rwork is correlated with Rfree so they would be reduced
> >> equally! Ther
I am trying to refine a neutron structure for someone and I have come across a
couple of things which I need help with.
I am struggling to get the occupancy refinement of the hydrogens/deuteriums on
the N-terminal nitrogens to behave right. Some of them get deleted by readyset
but the trick seem
It sounds like you have swapped the R-free set from being in phenix/xplor-style
to ccp4-style.
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On Tue, 25 Jun 2019 at 8:08, Tim Grüne wrote: Dear
Mirek,
it is a stubborn myth the Free-R flags need to be conserved. You can
simply regenerate a new set of f
For dynamics, you have probably already found VMD which is fairly easy to get
started with.
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On Mon, 1 Jul 2019 at 16:17, Mirella Vivoli Vega
wrote: Dear CCP Fo(r)lks,
I wonder if someone could help me about prediction servers or programs
or molecular dynam
For those who suffer from 80's nostalgia, I have worked-out a simple-man's way
of recovering the reflection data from this, now obsolete, format. Its here:
https://readingccp4lcffiles.blogspot.com
and it works for most of my VAX lcf files. Just thought this might be of
interest as the question h
Refining B-aniso's will clean up a difference map at that resolution.
Sent from Yahoo Mail on Android
On Tue, 9 Jul 2019 at 16:57, Bonsor, Daniel wrote:
#yiv3128113039 #yiv3128113039 -- _filtered #yiv3128113039 {panose-1:2 4 5 3 5
4 6 3 2 4;} _filtered #yiv3128113039 {font-family:Calibri;
I am trying to use a hex editor to read the unit cell parameters from the
headers of 80's VAX LCF files and I can definitely find them in front of the
column labels as six regularly spaced 32-bit floats. However, they seem to be
multiplied by a factor of 4 and the final corrected values of a, b,
Hello, can you get a good idea of the distance between the arginine sidechain
nitrogen and the phosphorus? It should be less than 2 A for a covalent bond. A
non-covalent complex will have an oxygen-nitrogen distance of about 2.8 A. If
the Arg is phosphorylated, then this residue is already one o
Hello David
I note that no changes will be allowed to the experimental data, but if there
are no experimental data, will the depositor be allowed to upload it/them,
without starting a new deposition? I'm finding a few reflection files that
ought to be deposited so that the corresponding structu
h the data were deposited (or corrected) much later than
the model. Sometimes more than 20 years. These kept the original PDBid.
Cheers,Robbie
On 2 Aug 2019 21:18, Jonathan Cooper
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
Hello David
I note that no changes will be allowed to the expe
A 10 year old laptop (64 bit) with Linux on it will be absolutely fine ;-)
Sent from Yahoo Mail on Android
On Wed, 14 Aug 2019 at 6:22, Matthew Bratkowski wrote:
Hi,
Can anyone recommend a good desktop computer for running crystallography
programs? I am looking for a Mac or Linux compute
You should be able to make a map with FFT by assigning F1 to your Fcalc and PHI
to your Phicalc, if not with the gui, then certainly with the command line. You
will need to make it cover your coordinates by ticking a gui option or running
extend in the command line.
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Sorry, it's mapmask, not extend anymore.
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On Tue, 20 Aug 2019 at 15:28, Jonathan
Cooper<0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: You should be
able to make a map with FFT by assigning F1 to your Fcalc and PHI to your
Phicalc, if n
When you open the map, in the window which comes up there is a little box to
tick which says "Is difference map?" in the lower left hand corner from memory.
Then it will display the -ve contours.
Sent from Yahoo Mail on Android
On Mon, 26 Aug 2019 at 15:34, Raymond Brown wrote: Hi
folks,
It would be useful to know the number of molecules per asymmetric unit and the
sequence similarity of the search model and target. There is always Molrep to
try which is good at NCS ;-
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On Thu, 29 Aug 2019 at 18:30, David Briggs wrote:
#yiv8743831735 #yiv87
at 18:41, Jonathan Cooper wrote:
It would be useful to know the number of molecules per asymmetric unit and the
sequence similarity of the search model and target. There is always Molrep to
try which is good at NCS ;-
Sent from Yahoo Mail on Android
On Thu, 29 Aug 2019 at 18:30, David B
I take it that the datasets are from different crystals. Are the
crystallisation conditions the same? I can't spot any signs of a difference in
indexing (but I may be wrong) so they look like different crystal forms. Are
the processing statistics good for both? Is this a case for molecular
repl
You should be able to get an idea of whether it has worked or not with viewHKL
in the old GUI e.g. find a few reflections with R-free flag zero in your old
dataset and note the indices. Then you can search the new dataset for these
reflections and see if they are still flagged zero. You may nee
I think LSQKAB can output a list of CA distances of two structures. Might be
easier to fit them first in Coot since LSQKAB can be a pig to run and you may
have to use the command line. You could then select the region(s) you are
interested in and use a spreadsheet or a script to calculate the RM
Sorry, I was wrong about using STDEV in Excel. Instead you would need to put
in a formula to calculate the root mean square of your distances. On
Tuesday, 17 September 2019, 15:14:02 BST, Jonathan Cooper
wrote:
I think LSQKAB can output a list of CA distances of two structures. Might
Adding chymotrypsin to your crystallisations in about 1:100 mass ratio with
your protein can help. You can quite easily find some papers on this method.
#yiv8007840479 -- filtered {panose-1:2 4 5 3 5 4 6 3 2 4;}#yiv8007840479
filtered {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;}#yiv800
This is a very good place to start:
https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html
Also recommend this one:
https://doi.org/10.1107/S0108767386099622
and Main, P. (1979) Acta Cryst. A35, 779-85 - the maths in this one are a bit
easier!
On Wednesday, 2 October 2019,
In i2 if you try the 'Prepare files for deposition' to make the cif's, it seems
to do a round of refinement, presumably to get the final stats, etc, but the
anisotropic B-factors seem to be ignored and are lost from the output file, as
far as I can tell. Hence, the R and R-free rise quite a bit.
Dear All
Please support the BCA winter meeting this year which, in a break from
convention, is being held at ESRF/ILL, Grenoble, France - as you know, a major
centre for structural biology research and infra-structure. This is an
experiment for the BSG committee, really, being in the spirit of
Dear All
For info, a few errata for my latest attempt to update Dennis Sherwood's book
'Crystals, X-rays and Proteins' (which is now firmly out in revised paperback
form ;-) can be found here...
http://www.ucl.ac.uk/~rmhajc0
Please let me know if anything else shows up.
Best wishes for now
Dear all
I have been asked by Randy for a reference for the following equation which
appears in Sherwood & Cooper:
http://www.ucl.ac.uk/~rmhajc0/truncate_no.jpg
... or in text form:
sigma(F) = sqrt(I + sigma(I)) - sqrt(I)
It is the equation which TRUNCATE uses to calculate sigma(|F|) if the use
Registration is now live for the British Crystallographic Association,
Biological Structures Group Winter Meeting 2016.
"Seeing the Wood for the Trees in Structural Biology."
The meeting will be held on Monday December 19th 2016 at Birkbeck College
London starting at 11.00 am.
The aim of the mee
Hello Tony
is that Asp-Gly? If so, it could be prone to succinimide formation. Check out
this paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323960/
and references therein!
Good luck
Jon.Cooper
--- On Thu, 25/4/13, Antony Oliver wrote:
From: Antony Oliver
Subject: [ccp4bb] Curious electr
BCA Biological Structures Group Winter Meeting 2016: "Seeing the Wood for the
Trees in Structural Biology." The meeting will be held on Monday 19th December
2016 at Birkbeck College, London starting at 11.00 am. The aim of the meeting
is to glimpse at some of the contemporary approaches for asse
Biological Structures Group Winter Meeting 2016: "Seeing the Wood for the Trees
in Structural Biology."
The meeting will be held on Monday 19th Dec 2016 at Birkbeck College, London at
11.00 am.
The aim of the meeting is to glimpse at some of the contemporary approaches for
assembling individual
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