Can anyone explain the rationale for treating the test set reflections
as 'unobserved' for the maps, even though they have perfectly good
observed Fo values? This doesn't make a great deal of sense to me!
Looking at the mtzdump output for the MTZ file output by Refmac, I
indeed note that for the
> You would also need to change the top line of the file so
> that it was something like "#!/bin/bash -f", though I would
> be more inclined to use a proper traditional Bourne shell for
> this and use "#!/bin/sh -f" and use "set"s and "export"s throughout.
That's not actually necessary for a 's
Hi Derek
The symmetry of the self-RF is explained in detail in the documentation for
POLARRFN, in fact I would advise you to use this because you can then plot
monoclinic space groups with the unique b axis along the orthogonal Z axis
(NCODE = 3) and then the symmetry is *much* easier to interp
> Indeed, I see the peak (69, 180, 180) but I don't find it in
> the list
> in the log file from Molrep. I thought that list was supposed to be
> exhaustive.
Yes you're right, it lists (111,0,180) twice, instead of listing it with
its symmetry mate as it seems to do with the other peaks.
Al
Hi, I think you'll find that if you work out the contribution from f' to
the density, in most cases it's not significant relative to the RMSD.
This will be particularly true for S which of course has a low value of
f' for all commonly used wavelengths. This must be true otherwise we
would observe
Simon,
You should always include H atoms in refinement whatever the resolution,
I can't think of any reason for not doing so. They are not refined
independently but 'ride' on the parent atom, so don't contribute to the
parameter and restraint counts, and as you say it is essential that they
are i
Victor
'P 21 2 21' *is* the conventional indexing if a <= b <= c, i.e. it's the
setting agreed for deposition of crystal structures by the IUCr and the
US National Institute of Standards & Technology (NIST) since 1983: it
just doesn't seem to have been agreed by a dwindling number of
individual
Hi Ethan
You could be right, see this paper:
http://physics.nist.gov/Divisions/Div842/Gp2/DUVMatChar/PDF/IntBiref.pdf
Cheers
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Ethan A Merritt
> Sent: 12 June 2008 15:46
> To: Multiple recip
wavelength) to detect the effect. However the
relevant theory goes back to Lorentz (1878) so it's not exactly new!
Cheers
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle
> Sent: 12 June 2008 17:50
> To: Ethan A Merrit
ved effect.
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Philippe DUMAS
> Sent: 12 June 2008 19:20
> To: Ian Tickle; CCP4BB@JISCMAIL.AC.UK
> Subject: RE: [ccp4bb] birefringent spacegroups
>
> Hello,
>
> A short comme
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Ethan Merritt
> Sent: 12 June 2008 19:41
> To: Multiple recipients
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] birefringent spacegroups
>
> But the ellipsoid is only a convenient approximation
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle
> Sent: 13 June 2008 11:20
> To: Ethan Merritt
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: RE: [ccp4bb] birefringent spacegroups
>
>
> > -Original Messag
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Sanishvili, Ruslan
> Sent: 17 June 2008 22:17
> To: Nave, C (Colin); CCP4BB@JISCMAIL.AC.UK
> Cc: Richard Gillilan
> Subject: RE: [ccp4bb] Structural importance of ordered water?
>
> Surely protein-wa
I would go along with Harry & friends, I used crystal cooling when I was
at Aafje Vos' Struktuurchemie lab in Groningen in 1972, when the
technique had already been in routine use there for at least 10 years,
in order to study compounds that are liquid at ambient temp (of course
it was custom-built
Hi U
Well if you can tell me the total number of atoms in your PDB file (NOT
counting any H atoms), I can estimate a range for the expected optimal
Rfree assuming your value of Rwork and the no of reflns in your working
set (~= 19x1715 = 32585 right?). If you have any NCS I can't promise my
estim
waters, then repeat the above test.
Hope this helps.
-- Ian
> -Original Message-
> From: U Sam [mailto:[EMAIL PROTECTED]
> Sent: 22 June 2008 04:47
> To: Ian Tickle
> Subject: RE: [ccp4bb] How many reflections for Rfree?
>
>
> Hi Ian,
> I have nearly 610
Hi Bernhard
This is OK, all it's saying is that if you generate by PG symmetry two
new reflection h' = hR' and h" = (-h)R" then the Bijvoet pair h' & h" is
symmetry-related to the Friedel pair h & -h.
The notation in your previous e-mail was somewhat imprecise, e.g. if h =
hR that implies that
Hi Matthew
It would be easy to edit the ligand restraint dictionary & make all the
sigmas very big (assuming the input CIF routines don't perform sanity
checks on the values!): that would make it unrestrained to all intents &
purposes. But when you say that unrestrained refinement is 'fine' wha
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of George M. Sheldrick
> Sent: 04 July 2008 13:42
> To: Matthew BOWLER
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Refmac unrestrained refinement on ligands only
> Perhaps what we
> really need a
Hi Clemens
It's complicated. If you unpack this bzip2/tar file it contains
's50.html' and some gifs showing the relevant equations.
Good luck!
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Clemens Grimm
> Sent: 09 July 2008 10:45
> To:
Hi Clemens
The relevant matrix algebra is all there in TLSANL, i.e. you could put
some code together based on that to do what you want, however there
isn't an option (even an undocumented one!) to do exactly what you want
and I don't know of any program which will do that. The math isn't
actually
on is applied separately to L and S.
Cheers
-- Ian
> -Original Message-
> From: Clemens Grimm
> [mailto:[EMAIL PROTECTED]
> Sent: 09 July 2008 14:20
> To: Ian Tickle
> Subject: RE: [ccp4bb] re-indexing, re-orienting and TLS-tensors
>
> Hi Ian,
>
> thanks f
Hi Pietro
This often happens if there's a chunk of data missing in the middle of a
dataset, due to ice rings say. Usually increasing the number of refls
per shell (SHELL keyword as you say) fixes this but in particularly bad
cases it may not. Can you send the standard output from scala, it may
b
Also while we're on the subject of novel crystallisation tricks, does anyone
out there have any first-hand impressions of this technique:
http://jjap.ipap.jp/link?JJAP/44/1365/
Cheers
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Isabel
Hi Phil
The rotation axis is the locus of points which the transformation leaves
unmoved, i.e. the eigenvector of the transformation matrix which has a
unit eigenvalue. So writing the transformation in homogeneous form for
convenience: x' = Sx you need to solve x' = x, or Sx = x, either
analytica
Hi David
No F23 has 4 alternate non-equivalent origins (i.e. invariant
amplitudes, different phases):
(0, 0, 0)
(1/4, 1/4, 1/4)
(1/2, 1/2, 1/2)
(3/4, 3/4, 3/4)
You can of course have other combinations of these by adding any of the
4 F-centring translations.
You can work this out from this tabl
Hi Yanming
You don't even need a shell script, there's a Unix command to do
precisely this: 'rename'.
Sadly usage does vary between distributions, e.g. Debian & RedHat based
distributions differ, so type 'man rename' and follow the instructions!
HTH!
-- Ian
> -Original Message-
> From
I think the problem is that Britannica, or even Wikipedia, is and has never
been the final arbiter of truth, I would put my faith in a specialist
publication such as:
http://books.google.co.uk/books?id=bwbCVCFPNI4C&pg=PA175&lpg=PA175&dq=%22karl+hasselbalch%22&source=web&ots=yHzTUiNE1g&sig=7JmNU-
Hi Jim
You can just run Truncate again, exactly as you did before, but this
time using your truncated.mtz file as input, since it contains the same
IMEAN/SIGIMEAN columns output by Scala. It will also give you another
output mtz file which should be identical to your input mtz (but I
haven't test
ost cause.
> >
> > George
> >
> > Prof. George M. Sheldrick FRS
> > Dept. Structural Chemistry,
> > University of Goettingen,
> > Tammannstr. 4,
> > D37077 Goettingen, Germany
> > Tel. +49-551-39-3021 or -3068
> > Fax. +49-551-39-22582
>
Hi David
One big problem you have here is that, depending on the low & high
resolution cutoffs and the completeness of your X-ray data, there will
be Fourier series termination and phase error effects on both the
electron density maxima and minima. The effects will be to reduce the
peak heights
This goes back to the issue I was raising, namely that ^2 (from the
Truncate output mtz F column) is not the same as Imeas (in the IMEAN
column) so you won't get exactly the same results from the Wilson plot,
particularly at high res where the average I/sigma is low. Since the
plot actually demand
-Original Message-
> From: Borhani, David [mailto:[EMAIL PROTECTED]
> Sent: 22 August 2008 15:10
> To: Ian Tickle; CCP4BB@JISCMAIL.AC.UK
> Subject: RE: [ccp4bb] How best to scale together absolute and
> Fo-Fc density maps?
>
> Thanks, Ian, this is very helpful. Data are 5
Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-3021 or -3068
> Fax. +49-551-39-22582
>
>
> On Fri, 22 Aug 2008, Ian Tickle wrote:
>
> > This goes back to the issue I was raising, namely that
> ^2 (from the
> > Truncate output mtz
ll (using a spline fit), not a linear Wilson plot
>
> Phil
>
>
>
> On 22 Aug 2008, at 20:30, Ian Tickle wrote:
>
> > This indeed raises the question of whether the assumed Wilson
> > distribution is valid, and it's another point I was in fact going to
>
absolute scale. This isn't necessary, but it doesn't hurt
>
> There's no reason why truncate shouldn't give a "best"
> estimate of |F|
> ^2 but I'm not sure why you would want this. I would think that
> refinement is better done agains
del.
>
> This is of course a purely theoretical discussion, there is no
> need for anyone to retract their published structures.
>
> Best wishes, George
>
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr.
Hi Rajan
You don't really need a program: e.g. if there are N non-H atoms
refined, then there are 4N params (isotropic B) or 9N (aniso). TLS adds
19 params per group to the isotropic count. You count unique
reflections.
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:
OTECTED]
> Sent: 29 August 2008 13:47
> To: Ian Tickle
> Subject: RE: [ccp4bb] Ratio of Number of Reflections to
> Number of restrained Parameters
>
> Angle/bond/planarity restraints (because they are
> experimentally determined
> from prior data) should count as
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Jon Wright
> Sent: 08 September 2008 21:29
> To: Borhani, David
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] truncate ignorance
>
> Borhani, David wrote:
> > ...
> > but I think pretty much eve
But there's a fundamental difference in approach, the authors here
assume the apparently simpler prior distribution P(I) = 0 for I < 0 &
P(I) = const for I >= 0. As users of Bayesian priors well know this is
an improper prior since it integrates to infinity instead of unity.
This means that, unlik
Having read the remainder of the paper more carefully I note that the
authors do go into an extensive discussion about Jeffreys (which they
don't recommend) and Wilson priors, which indeed overcome my objection
to the use of the improper prior. They conclude that the simpler
expression is adequate
> -Original Message-
> From: Bart Hazes [mailto:[EMAIL PROTECTED]
> Sent: 08 September 2008 23:44
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] truncate ignorance
>
>
> How a seemingly innocent question can explode ...
Well the
For comparison I repeated my previous calculation using the flat
(non-Wilson) prior that you suggested (you would get the same results
using the F&W method in the limit of an infinite WDP). So now the
results are indeed totally independent of the WDP - but IMO the results
are also completely count
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On
> Behalf Of Eleanor Dodson
> Sent: 09 September 2008 17:11
> To: William G. Scott
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] truncate and anisotropy
>
> I dont think you need to worry much about the stron
Hi, it's not clear why this should be necessary in general since
$CLIBD/atomsf.lib contains entries for both Zn & Zn+2:
Zn
30301.304100
14.0743007.0318005.1625002.41
3.2655000.233300 10.316299 58.709702
-
sed Cl should be 'Cl-1' and is listed in atomsf.lib as such.
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Roger Rowlett
> Sent: 11 September 2008 16:24
> To: Ian Tickle
> Cc: Patrick Loll; CCP4BB@JISCMAIL.AC
I would have thought that it would always be a good idea to refine only
the occupancies in the first few cycles and only refine co-ords & B
factors once the occupancies have settled down to sensible values. But
in that case wouldn't the Fcalc's be linearly dependent on the
occupancies so the occup
27;t
agree here, surely the best way is to come up with a PDF of J that as
accurately as possible describes the anisotropy and use that in the F&W formula
(though I admit I don't have any concrete suggestions!).
In summary I think that although the S&D method may be useful in cases of
Hi Jan
We had this problem, I think it's because the character strings used to
store pathnames are only 80 chars long, so if you have a long pathname
(you didn't show your full pathname!) then it has a problem. You can
either fix the program, or do as we did make a soft link in the current
direct
All - I've been trying to track down a paper (or papers) where it was
shown that the epsilon values (symmetry factors) for space groups with
pure rotation axes are not integers as is usually assumed (but still
integers for screw axes). It's almost certainly in Acta Cryst.,
probably in the 60's or
Sorry I should have copied this to the BB as it may be of general
interest:
-Original Message-
From: Ian Tickle
Sent: 17 September 2008 11:05
To: 'Jan Dohnalek'
Subject: RE: [ccp4bb] Topp fails: TOP: Open failed: File:
/people/./myfile.pdb
OK try this one: looking at the
But what connectivity would be implied by descending numbers: the order
in the file or the order of the numbering? I assume the former,
otherwise what would be the point of having descending numbering? And I
wonder how many programs would baulk at it (or even at ascending
negative numbers?).
--
ually more
> complicated than
> it looked like in the first place?
>
> Thanks
> Clemens
>
> Ian Tickle schrieb:
> > Clemens,
> >
> > One thing I should have pointed out, though you may have realised it
> > already: you will most likely want to keep
Grimm
> [mailto:[EMAIL PROTECTED]
> Sent: 23 September 2008 16:41
> To: CCP4BB@JISCMAIL.AC.UK
> Cc: Ian Tickle
> Subject: The mystery of the S-tensor WAS: re-indexing,
> re-orienting and TLS-tensors
>
> Dear all,
>
> a few weeks ago I was wondering how to apply a
This goes back to my previous idea about using the Bayesian estimates
( & sig()) of I & sig(I) in the refinement instead of the measured
ones. This would remove any objection to using negative observed
intensities, though it's hard to see what exactly the objection is.
Basically you're just moving
In fact there's another good reason not to use H3 etc when you mean R3:
the H lattice symbol is already in use to mean something completely
different! - namely H-centring in *trigonal & hexagonal* (i.e. *not
rhombohedral*) space groups such as P3, P3/1 etc & supergroups, so e.g.
H3 is actually a su
easier to read), this could have been handled by mapping internally
stored versions without spaces to the user-visible versions when
printing log files etc.
-- Ian
> -Original Message-
> From: Bernhard Rupp [mailto:[EMAIL PROTECTED]
> Sent: 28 October 2008 05:22
> To: Ian Tick
All - I was just in a discussion about TLS and one thing that came out
that I hadn't been aware of is that for the Biso restraints Refmac
restrains the difference between the 'residual' Bs, i.e. with the TLS
contributions subtracted, not the 'total' Bs. Now it seems to me that
this isn't quite c
Hi Pavel
I think Ethan made my point very nicely, so I don't really have much to
add, except maybe a concrete example will help. Let's keep it as simple
and ideal as possible: I hope you'll agree that any proposed method has
to at least work perfectly in the ideal case before you try to apply i
Actually on further thought I see that the problems associated with
restraining residual Biso's are even more serious, and even my
suggestion of ensuring that there's a flexible linker would not get
around it. Suppose you have a domain with an associated TLS group
connected to a flexible linker wh
rom my own experience I know
that a typical co-ordinate uncertainty at 1.5 A resolution is ~ 0.2 Ang
for unrestrained refinement, but ~ 0.02 Ang for restrained - an order of
magnitude less! Would you say the large uncertainties from the
unrestrained refinement are 'distorted' by the use of res
Hi Huiying
At 2.1A I would be very surprised if you see any density for the H atom
in which case the refinement is not going to move it out of the plane
whatever weight you give the torsion restraint. To answer your earlier
questions the period of a torsion restraint is the number of energy
minim
still pushed OH into the
> plane. I wonder
> if there are other tricks that can impose the restraint for
> this torsion
> angle.
>
> Best,
> Huiying
>
> On Thu, 4 Dec 2008, Ian Tickle wrote:
>
> > Hi Huiying
> >
> > At 2.1A I would be very
I go along with all Eckhard's cautionary advice & particularly his
suggestion that all restraint info be deposited, as without that it's
impossible to reproduce the experiment! - the restraint info (both
target values & weights or s.d.'s) is literally just as important as the
X-ray data. The only
But that only means that the SF contribution from that pair of molecules in the
unit cell is zero for (00l) l=odd reflections. Depending on the
crystallographic symmetry (e.g. if it were 3-fold or higher order) there may be
other pairs for which the SF contribution is non-zero for all (00l) (b
think we've reached that stage yet!
-- Ian
> -Original Message-
> From: Jim Pflugrath [mailto:jim.pflugr...@rigaku.com]
> Sent: 15 December 2008 15:52
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] About system absence in P4222?
>
>
s complicated. However,
> to do the math with
> --
>
> Plug the coordinates (x,y,z) and x+tx, Y+ty,
> z+tz) into the
>
>
> SF equation.
>
> --
> is exactly the only way to test it.
>
> Li
earle 1-240
> 2240 Campus Drive
> Evanston IL 60208
> lab: 847.491.2438
> cel: 773.608.9185
> email: j-kell...@northwestern.edu
> *******
>
> - Original Message -
> From: "Ian Tickle"
> To:
> Sent: Monday, Dec
Hi Simon
I think I can say without fear of contradiction that this is still a
subject under debate, so I'm not at all surprised that the referees
can't agree between themselves! I think there are actually two answers
to your question: (1) what is the formally correct answer, and (2) what
is the a
Hi Alun
I've never seen a soaked ligand-bound structure that's truly isomorphous
with the native - simply soaking & freezing the crystal is virtually
guaranteed to introduce very serious non-isomorphism, e.g. up to 5%
change in one or more cell parameters. At least, we always have a MR
step to so
; to transfer initial free R assignment to any new data sets or to
> isomorphous data sets such as substrate complexes.
>
> Thanks,
>
> Alun.
>
> Ian Tickle wrote:
> > Hi Alun
> >
> > I've never seen a soaked ligand-bound structure that'
All, something for you to think about over the Study Weekend - sorry I
can't be there with you this time :-( :
I was recently asked whether a formal derivation of the expression we
use for the 'minimally biased' difference Fourier coefficient, i.e.
delta-Fm = mFo-DFc, is published anywhere, and I
bove it is clear
that FWT and DELFWT have been computed using FC_ALL not FC, so that's
why I actually used the FC_ALL value (182.9) in my example.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of
All - I didn't get a single response to my posting last week
(https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0812&L=CCP4BB&T=0&O=D
&X=512817322E87355F7F&Y=i.tickle%40astex-therapeutics.com&P=266420)
concerning the formulae that are widely used for the 'minimally-biased'
Fourier and difference
I was taught 'structure amplitude' - makes perfect sense to me! Why
does 'structure amplitude' make any less sense than 'structure factor'?
It also clearly made sense to Phil Coppens, a crystallographer of
considerable repute, see ITC Vol. B (2nd Ed.), sect 1.2., p.10: 'The
Structure Factor'. To
ight said. "The song really is 'A-sitting
On a Gate': and the tune's my own invention."
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Dirk Kostrewa
> Sent: 12 January
y
disagree on that point), provided it is pointed out that there is
precedent for an alternative name for the object in question, and
perhaps a reference should be made to the original authoritative
definition.
Cheers
-- Ian
> -Original Message-
> From: Gerard Bricogne [m
clearly bucking the
majority trend!). I think all one can conclude from that is that both
terms are equally clear to the majority of authors and readers alike.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf O
Well according to Google this paper (JCS, 1936) contains the phrase
"magnitudes of the structure amplitude factors (F)":
http://www.google.co.uk/search?hl=en&q=%22magnitudes+of+the+structure+am
plitude+factors%22&btnG=Search&meta= .
It seems that "structure amplitude factor" is what we have now
a
> -Original Message-
> From: marc.schi...@epfl.ch [mailto:marc.schi...@epfl.ch]
> Sent: 12 January 2009 22:35
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] structure (factor) amplitude
>
> Ian Tickle wrote:
>
> OK, limiting the
Jacob
I suspect it's derived from the card game "Queen of Spades", also called
"Hearts", but is apparently originally from China where it is called
"Gong Zhu". I (mis)spent a lot of time in my youth playing it! This
site explains the rules: http://www.pagat.com/reverse/gongzhu.html .
The game is
Hi Margriet
It's almost certainly due to diffuse scattering as a result of
correlated atomic displacements. See this:
http://www.nature.com/nsmb/journal/v1/n2/pdf/nsb0294-124.pdf .
Are they lines or sheets, in other words do they appear only on one
image, or are they also on adjacent images, i.e
Hi, it's clearly not a detector problem (at least not an obvious one!),
since the 'lines' clearly follow the *curved* path of the reciprocal
lattice lines as they are projected from the Ewald sphere onto the
detector. A saturated pixel would presumably affect other pixels only
in the same row and
Hi Herman
Aren't detwinning methods appropriate only in the case of true twin domains
which are larger than the X-ray photon correlation length in order for the
assumption to be valid that |F|^2 from each domain can be summed? This
wouldn't give rise to the apparent 'diffuse scatter' phenomeno
Rana, to a large extent this depends on what you what to do with the
delta-F's afterwards (you didn't say). If all you want to do is
calculate a map, Patterson or Fourier, (which is probably what we do
most of the time with delta-F's) then you don't need to calculate the
difference as a separate s
Bernhard
Yes I stand corrected, 'coherence length' it is. I think I did mean
'coherence' and not 'correlation', it's just that I had 'correlation' on
my mind from something else I was doing. What I need is a 'concept
checker' in addition to a spelling & grammar checker!
-- Ian
> -Original
Clemens, I know we've had this discussion several times before, but I'd
like to take you up on the point you made that reducing Rfree-R is
necessarily always a 'good thing'. Suppose the refinement had started
from a point where Rfree was biased, e.g. the test set in use had
previously been part of
same data of course), making your model overfitted
after the fact!
Cheers
-- Ian
> -Original Message-
> From: George M. Sheldrick [mailto:gshe...@shelx.uni-ac.gwdg.de]
> Sent: 16 February 2009 11:24
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Francis E Reyes
> Sent: 18 February 2009 23:32
> To: ccp4bb@jiscmail.ac.uk
> Subject: educational opportunity: Difference between SIRAS and SAD?
>
> (here scattering and dispersion
Hi Anita
A bug was reported with that version of Refmac, though I've no idea if that
would cause your problem: you should upgrade to the latest version from the
York website.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On
Hi Bernhard
Did you try this:
http://download.corruptedfilerepair.com/post/2008/07/02/clexe-Download-F
ile-clexe.aspx
(note that after clicking on the "Download Link #7: Download CL.EXE"
link, the actual download link in case it doesn't start automatically,
which it didn't for me, is below the a
Bernhard
There's the related issue of how to optimally treat the *test set*
reflections, i.e. perfectly good measurements but not used (in
refinement that is). The various program authors seem to treat these
quite differently, e.g. Refmac AFAICS treats them exactly like
unobserved for the maps an
Hi Garib
Does this answer your question (see final paragraph):
http://www.nature.com/nature/journal/v448/n7154/full/nature06102.html
Best
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Garib Murshudov
> Sent: 18 March
Hi James
I think the answer to your question about the 'R-factor gap' is easy to
answer (but not so easy to solve!). It's obviously due to the
inadequacy of our models, particularly with regards to thermal motion
(anisotropy, anharmonicity etc), disorder & motion correlation/diffuse
scatter, also
Felix
I would be very surprised if anyone could calculate the expected Rfree
in this case with any degree of reliability, since it seems to have been
refined with a combination of TLS and rigid-bond/sphericity anisotropic
ADP restraints. Taking account of restraints, particularly thermal ones
whi
Hi Kristof
The trivial, and it turns out only, answer is "as many as it takes to
converge". Unfortunately for everyone carrying out optimisations, or
indeed almost any kind of computation, Alan Turing proved (1936) -
Google for "Turing halting problem" - that a general algorithm to solve
the halt
But aren't the bump restraints re-evaluated at each iteration? That was
my understanding (but I could be wrong), after all it's not a big deal
to compute interatomic distances. One contribution that is not
re-evaluated every iteration but only at iteration 1 is (I believe, but
again I could be wr
Hi Jason
Type 'set verbose' (without the apostrophes) and trying sourcing again,
it should stop just before the offending line.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Phan, Jason
> Sent: 27 March 2009 16
-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Phan, Jason
> Sent: 27 March 2009 18:52
> To: Ian Tickle
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: RE: [ccp4bb] Problem sourcing
>
> Dear Ian,
>
> I got bumped out at this line:
>
> Se
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