Hi Graeme
No it looks like the problem is some network setting on David's side since
I can submit David's data to the STARANISO server with no problem. The
only thing to be aware of is that when submitting scaled unmerged data the
checkbox "*Check* here if the data are unmerged but already scaled
It's a Wiki so anyone can edit it. I think you just have to create an
account here:
https://dictionary.iucr.org/index.php?title=Special:CreateAccount&returnto=Real-space+correlation+coefficient
Note that you must have an entry in the World Directory of
Crystallographers, otherwise your Username
A file does not have a handedness, it's just a list of numbers. So the
pedantic answer is that since it doesn't have a handedness you need do
nothing to change it!
I assume that what you mean is that you want to change the handedness of
the _visual interpretation_ of the file. That's a different
Hi, that would have to be a very old map! I remember implementing the
auto-byte swap for VMS (necessary as we had both a Convex C220 running Unix
and a VAX 11/750)!
In fact the Convex was rescued from scrap by Jim Austin and is still
working: http://www.corestore.org/convex.htm
Cheers
-- Ian
gh... School of Pharmacy rings a
>> bell??
>>
>> None of this matters, but I just thought you might like to practice some
>> 'big-iron' byte-swapping again, and if so, York is the place to go, after
>> covid-19, of course ;-0 ;-0
>> On Friday, 15 May 2020
tice some
> 'big-iron' byte-swapping again, and if so, York is the place to go, after
> covid-19, of course ;-0 ;-0
> On Friday, 15 May 2020, 10:47:40 BST, Ian Tickle
> wrote:
>
>
>
> Hi, that would have to be a very old map! I remember implementing the
> a
Hi Robbie
I don't see that anisotropic truncation has anything to do with the low
spherical completeness as compared with the info in the co-ordinate file.
Yes the spherical completeness after anisotropic truncation will be
reduced, but why would it cause it to become inconsistent with that
report
Also agree, see http://staraniso.globalphasing.org/deposition_about.html .
Cheers
-- Ian
On Sat, 30 May 2020 at 15:58, Robbie Joosten
wrote:
> I fully agree. Unfortunately, not everyone does that so cases like I
> described will keep appearing.
>
> Cheers,
> Robbie
>
> On 30 May 2020 16:40, E
Hi Joao
For all CCP4 programs you need to source your CCP4 setup script.
Cheers
-- Ian
On Mon, 15 Jun 2020 at 15:29, Joao Ramos wrote:
> Dear CCP4bb,
>
> I'm trying to obtain RSC metrics using the CCP4 program EDSTATS for a
> Phenix refinement job, in order to have a more reliable analysis o
; error
> message (screenshot attached) when trying to run MTZFIX.
>
> Best regards,
> Joao Ramos
>
> Ian Tickle escreveu no dia segunda, 15/06/2020 à(s)
> 16:57:
>
>>
>> Hi Joao
>>
>> For all CCP4 programs you need to source your CCP4 setup
given read
permission).
Cheers
Ian
On Mon, 15 Jun 2020, 19:09 Ian Tickle, wrote:
>
> Hi Joao
>
> The top of the page was cut off in your screenshot so I can't see the
> command line you typed. It would be better to copy/paste the entire text,
> including the input comma
essage saying that mtzfix cannot find the labels. I'm using a mtz file
> from a refinement job in Phenix.
>
> Best regards,
> Joao Ramos
>
> Ian Tickle escreveu no dia terça, 16/06/2020 à(s)
> 09:39:
>
>> Hi João
>>
>> In cases like this it's alwa
I agree about RAID but I would go a lot further. There seems to be some
confusion here over the correct meaning of 'redundant' as used in a
scientific context. I don't think looking it up in an English dictionary
is very helpful. So as has been mentioned the non-scientific and rather
imprecise m
“Redundancy” to “Multiplicity” in Scala,
> later in Aimless, after I was taken to task by Elspeth Garman with the
> argument as stated, that if it’s redundant why did you bother to measure it?
>
> (this one could run and run …)
>
> Phil
>
> > On 30 Jun 2020, at 14:07, Ian Ti
eumann by at least 4 centuries.
>
> One of the first instances of its use was in the 1500s, due to a migrant
> scientist working in Denmark and Prague, Czech Republic: Tycho Brahe,
> whom "the divine goodness [had] given to us" (Kepler).
>
> Best regards,
> Navd
Well I very much doubt that many software developers are going to trawl
through all their code, comments, output statements & documentation to
change 'redundancy' or 'multiplicity' to 'MPR' or whatever terminology is
agreed on (assuming of course we do manage to come to an agreement, which I
doubt)
Hi,
There's one big difference between macromolecular and small molecule
refinement: except at ultra-high resolution the bond lengths in the former
are almost always strongly restrained, whereas those in the latter are
almost without exception completely unrestrained (except possibly bond
lengths
e
>
> > -Original Message-
> > From: CCP4 bulletin board On Behalf Of Ian
> > Tickle
> > Sent: Wednesday, July 15, 2020 20:25
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Quote source inquiry
> >
> >
> > Hi,
> &g
Hi David
The problem is that the PDB incorrectly used the H lattice symbol (without
consulting any crystallographers AFAIK) for the hexagonal R-centred cell
when it had already been in use for many years for the triply-primitive
setting of P3, so now we have this confusion between MX & XRD/powder
Hi Eleanor
H3 #143 is (and always has been) a triply-primitive cell setting of P3.
http://img.chem.ucl.ac.uk/sgp/large/143bz1.htm
Cheers
-- Ian
On Wed, 22 Jul 2020 at 14:42, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> But surely P3 symmetry ' cell ( a,a,c 90 90 1
The important take-home message in this excellent article is surely the
conclusion:
"The significant amount of programming effort and user frustration caused
by the H3 and H32 space-group symbols is a good example of how time can be
lost by not adopting long-established standards. This is not mea
The original reference for the H cell is the very first edition of Int.
Tab.:
Hermann, C. (1935). Internationale Tabellen zur Bestimmung von
Kristallstrukturen. Berlin: Gebrueder Borntraeger.
Cheers
-- Ian
On Wed, 22 Jul 2020 at 17:34, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail
Hi Christian
I wouldn't worry: if the density is clear that nails it. You didn't say
whether this is a soak or co-crystallization. I assume the former since
you mention solvent channels. In my experience this is much more likely in
the case of soaks, which can often (though not always) be ratio
Dear All
I just downloaded a PDB file (7A5V) from the EBI server, tried to run
Refmac on it and got the error:
ERROR: in chain A residue: 279 different residues have the same number
There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
===> Err
s no clean solution for this and I imagine this problem goes
>> very deep into the internal representation of the model in REFMAC. That
>> said, 1 in 6 missing PDB-REDO entries is caused by this problem, so a
>> solution would be very welcome.
>>
>> Cheers,
>> Robbi
3.892 151.967 0.50 59.05
> N
>
> We deposited the PDB file that could be handled by Refmac5, but
> insertion code was replaced with alt loc code in the annotation
> process.
>
> Please also note that the NCS constraint function with evaluation of
> nonbonde
There was a little bit of press-release hype: the release stated "a score
of around 90 GDT is informally considered to be competitive with results
obtained from experimental methods" and "our latest AlphaFold system
achieves a median score of 92.4 GDT overall across all targets. This means
that our
ell they overlap.
>
> -- Tristan
>
> * There's one more thorny issue when you get to this level: it becomes
> more and more possible (even likely) that the prediction gets some things
> right that are wrong in the experimental structure.
> -------------
things
> right that are wrong in the experimental structure.
> --
> *From:* CCP4 bulletin board
> on behalf of Ian Tickle
>
> *Sent:* 08 December 2020 13:04
> *To:* CCP4BB@JISCMAIL.AC.UK
>
> *Subject:* Re: [ccp4bb] External: Re: [ccp4bb]
there is _no_ anom signal but I forgot the details, sorry ...
>
> It is derived from the mean absolute error (cf. p414 in Chapter 8 of BMC,
> with help of Ian Tickle), and holds for unmerged data. A reasonable good
> indication where to set the cutoff in practice is to look at the sit
Hi Bernhard
I gave up trying to use CIF2MTZ in the STARANISO server over a year ago. I
agree with Marcin that his GEMMI program is the way to go. It does
everything you need and Marcin is very quick to respond to any issues.
The problem is that there are alternate settings in the PDB so the so
Frank,
Point #1 - fair point; the reason Rfree is popular, though, is because it
> is a *relative* metric, i.e. by now we have a sense of what "good" is. So
> I predict an uphill fight for LLfree.
>
Why? I don't see any difference. As you say Rfree is a relative metric so
your sense of what 'g
hat is the upper limit 100 or
> thousand or million according to my understanding, its more logical to
> stop the refinement when over refinement is taking place (when R and Rfree
> are going in opposite directions and LLG is stabilized )
>
>
> On Fri, Aug 26, 2011 at 4:01
On Mon, Aug 29, 2011 at 7:53 AM, Nat Echols wrote:
> On Sun, Aug 28, 2011 at 7:23 PM, Jacob Keller <
> j-kell...@fsm.northwestern.edu> wrote:
>
>> are there any additional problems or known issues running ccp4 or
>> other xtal software on windows 7 (beyond those of Vista, etc.?)
>
>
> Phenix, ARP/
Hi John,
There's some by now fairly ancient tutorial material on the SRF (though of
course the theory hasn't changed) here:
http://www.ccp4.ac.uk/dist/ccp4i/help/modules/appendices/mr-bathtutorial/mrbath2.html#section2.8
(and the following section 2.9) and here:
http://www.ccp4.ac.uk/dist/ccp4i
Hi Rex
I would assume it's the RMS deviation of the rotation function value from
the mean. If so then it's defined in the same way as the "population
standard deviation" as given here:
http://en.wikipedia.org/wiki/Standard_deviation
Cheers
-- Ian
On Fri, Sep 9, 2011 at 4:20 PM, REX PALMER wrot
ally does this or not
would require an examination of the source code, though it's probably
quicker to ask Eleanor!
Cheers
-- Ian
On Fri, Sep 9, 2011 at 5:26 PM, Ian Tickle wrote:
>
> Hi Rex
>
> I would assume it's the RMS deviation of the rotation function value from
>
Hi, it depends what you mean by 'different'. The SUs of the new set are
much lower than the old values (0.8 deg vs. 3.0) so one would assume that
these are improved estimates based on new data. The difference between the
old and the new is (108.4 - 107.8) = 0.6 deg with a SU of the difference of
On Tue, Oct 4, 2011 at 11:21 AM, Adam Ralph wrote:
> Dear Brigitte,
>
>
> Looking at the formulae it could be possible to get those results.
> Take an example
> below
>
>
> Rho_cal = -0.11, 0.0, 0.05, 0.05
> Rho_obs = -0.08, 0.01, 0.04, 0.04
>
>
> R-fac = 0.02/0.0 = undefined
Ooops (.03+.01+.01+.01)/(.19+.01+.09+.09) = .16
-- Ian
On Tue, Oct 4, 2011 at 12:22 PM, Ian Tickle wrote:
> On Tue, Oct 4, 2011 at 11:21 AM, Adam Ralph wrote:
>
>> Dear Brigitte,
>>
>>
>> Looking at the formulae it could be possible to get those result
On Tue, Oct 4, 2011 at 4:41 PM, Eleanor Dodson wrote:
> OK
>
> So the ATOM TYPE has ZN O C S etc in column 77/78 and the +2 etc in 79/80
>
> Is there any documentation for this?
>
> E
Yes, see:
ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf
Though this has been the forma
On Tue, Oct 4, 2011 at 7:14 PM, wrote:
> Hi Adam and Ian,
>
> Thanks for your help. If I re-calculate the R-factors with the correct
> absolute values I get more reasonable values. However, I'm still a bit
> confused because the output given by the Overlapmap program is structure
> factor value
On Wed, Oct 5, 2011 at 11:03 AM, Adam Ralph wrote:
> Hi Brigitte,
>You are correct, the columns labeled Fobs and Fcal refer to density. The
> columns should be: averaged density for Obs and Cal for the main chain, then
> averaged density Obs and Cal for the side chains. I have included a vers
ap's residue
> correlation but did
> not work properly.
>
> Adam
>
>
>
> - Original Message -
> From: "Ian Tickle"
> To: "Adam Ralph"
> Cc: CCP4BB@jiscmail.ac.uk
> Sent: Wednesday, 5 October, 2011 11:36:30 AM
> Subject: Re: [cc
On Wed, Oct 12, 2011 at 1:35 AM, James Holton wrote:
> My list has 8 different allowed
> shifts for I222, but I assume this is because the 0,0,1/2 shift is
> part of a symmetry operator. I guess it is a matter of semantics as
> to wether or not that is an "allowed shift"?
>
> James, the (0,0,1/2
Hi Phil
My understanding is that when the B factor was devised it was believed
that it wouldn't represent any physical reality and was initially at
least widely regarded as a "garbage dump" for errors. So it made no
difference whether or not it was related to the natural length in
reciprocal spac
Yet Uaniso's are multiplied by 1 and stored as integers with no problem!
-- Ian
On Thu, Oct 13, 2011 at 1:44 AM, James Holton wrote:
> I think the PDB decided to store "B" instead of "U" because unless the
> B factor was > 80, there would always be a leading "0." in that
> column, and that w
Hi Stephen
You just multiply the Uij values in the ANISOU record by 8pi^2/1.
This begs the question why you want the Bij values in the first place
(since the Bij's don't correspond to any physical parameter)? Note
that TLS parameters are on the same scale as U, not B.
Cheers
-- Ian
2011/1
Hi Kavya
The resolutions of the structures mentioned in the paper were only
examples, the Rfree/-LLfree minimisation method (which are actually
due to Axel Brunger & Gerard Bricogne respectively) does not depend on
resolution.
If the structures are already solved & refined, you don't need to do
a
ers.
>
> Thanking you
> With regards
> M. Kavyashree
>
> -CCP4 bulletin board wrote: -----
>
> To: CCP4BB@JISCMAIL.AC.UK
> From: Ian Tickle
> Sent by: CCP4 bulletin board
> Date: 10/14/2011 12:34PM
> Subject: Re: [ccp4bb] Optimisation of weights
>
>
nds) is around 0.5 for typical resolutions (a bit
lower for low resolution, a bit higher for very high resolution) it
won't affect interpretation of maps etc.
Cheers
-- Ian
On Fri, Oct 14, 2011 at 9:37 AM, Ian Tickle wrote:
> It must be the same complete model that you refined previously, I
Hello all, some Fortran developer out there must know the answer to
this one. I'm getting a "forrtl: severe (41): insufficient virtual
memory" error when allocating dynamic memory from a F95 program
compiled with Intel Fortran v11.1.059. The program was compiled on an
old ia-32 Linux box with 1Gb
as the initial weights are "in the same ball park",
> so that your RMSZ(bonds) is around 0.5 for typical resolutions (a bit
> lower for low resolution, a bit higher for very high resolution) it
> won't affect interpretation of maps etc.
>
> Cheers
>
> -- Ian
>
&g
> Try the GNU (compiler) and see what it says. ;)
Hi Francois - I won't bore you with the long list of compiler errors
that gfortran gives with my code (ifort compiles the identical code
without error and up until now it has worked just fine on both 32 & 64
bit machines as long as don't try to all
> Yes, the weight mentioned in the paper was
> weight matrix, but the one i used was the
> option under "Refinement parameters- weighing
> term (when auto weighing is turned off)".
> But If I really wasnt to change the weight matrix
> where should I change (in the code?)?
No, the weights referred
Hi, currently Refmac writes the wrong info for the low resolution
cutoff, for example:
REMARK 3 PROGRAM : REFMAC 5.6.0119
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 84.35
In contrast Shel-X
Hi, personally I didn't find that changing scattering factors for Se,
Br, I etc made a big difference to the maps. The more likely
explanation seems to be site occupancy disorder due to
radiation-induced breaking of covalent bonds, in which case you need
to refine the occupancy. But maybe it's a
James, this doesn't take the effect of resolution cut-offs into
account, right? You appear to be assuming that you have data to
atomic resolution (~ 1 A) or better. The integral of the scattering
factor should be confined to the experimental resolution range,
otherwise it's not going to be very r
I can think of at least one good reason: you might want to optimise
the weights using different starting values. In that case there's no
need to look at the maps until the end. But as Eleanor says you can
always delete them. I would do the weight optimisation with a
customised script, so this wo
On Mon, Nov 21, 2011 at 10:23 AM, Eleanor Dodson wrote:
> Just a plea for less molecular replacement.
>
> If you get a new crystal of a known protein with the same cell dimension as
> youur old crystal, the most likely scenario is that it has the same group,
> and you really should not try MR - u
Rajesh
I use adxv (as well as xemacs, xdsview, imosflm, hklview, ipdisp etc)
over ssh/Cygwin X11 from Windows XP to a Centos (like RedHat) server
with no problems at all.
I suspect your xming either just doesn't have the requisite X11 libs
or somehow they have not gotten installed on your system
()'
>> > Warning: String to TranslationTable conversion encountered errors
>> > Warning: translation table syntax error: Unknown keysym name:
>> > osfSelect
>> > Warning: ... found while parsing ':osfSelect: KeySelect()'
>> > Warning: Strin
On 22 November 2011 22:04, Pius Padayatti wrote:
> Rajesh,
> The fonts error please follow the guidelines from following link
>
> http://www.scripps.edu/~arvai/adxv.html
OK the fonts you need are the ones mentioned above (in
http://www.scripps.edu/~arvai/adxv/fonts.tar.gz), BUT the installation
i
also an obvious possibility as Anthony said, and I would
follow his sensible advice.
Cheers
-- Ian
Cheers
-- Ian
On 23 November 2011 10:58, Eleanor Dodson wrote:
> I wish I could answer this!
> One possibility is that the side-chain B values are too tightly restrained -
> Ian Tickle re
On 23 November 2011 07:54, Careina Edgooms wrote:
> I have a question about a 2F0-Fc difference map that I calculated with Refmac.
On 23 November 2011 15:40, Nat Echols wrote:
> The negative density around Met S could be radiation damage.
But you wouldn't expect to see -ve density in the 2Fo-Fc
ained -ve density in the 2Fo-Fc map or in the Fo-Fc map?
Cheers
-- Ian
On 23 November 2011 16:03, Nat Echols wrote:
> On Wed, Nov 23, 2011 at 7:57 AM, Ian Tickle wrote:
>> On 23 November 2011 07:54, Careina Edgooms wrote:
>>> I have a question about a 2F0-Fc difference map
Simon
This appears to be a csh or tcsh script: if so the first line must be
"#!/bin/csh" or "#!/bin/tcsh", otherwise it takes it to be a sh
script.
Cheers
-- Ian
On 2 December 2011 14:45, Simon Kolstoe wrote:
> Hi there,
>
> I've got a text file with multiple conformations of a ligand that has
On 13 December 2011 17:59, James Holton wrote:
> A small but potentially important correction:
>
> FC_ALL PHIC_ALL from REFMAC are indeed the calculated structure factor of
> the coordinates+bulk_solvent, but AFTER multiplying by the likelihood
> coefficient "D" (as in 2*m*Fo-D*Fc ). So, if you s
Hi Bernhard
So what's new? See
http://ccp4bb.blogspot.com/2011/11/pdb-header-info-wrong.html
(17-Nov-11).
Cheers
-- Ian
On 2 January 2012 06:58, Bernhard Rupp (Hofkristallrat a.D.)
wrote:
> Dear Developers,
>
> it seems to me that at least Refmac 5.6.0117 does not report the actual
> lowest
On 9 January 2012 06:13, Shveta Bisht wrote:
> Dear all
>
> I have generated a refmac cif file for a molecule using PRODRG. I used
> JME editor to draw the molecule and ran PRODRG online with the
> options: Chirality-Yes, Charges-Reduced and EM-Yes. Please check the
> attachments for the molecule
Jacob,
Actually the R factors including the Bijvoet pairs would be higher,
because the uncertainties in F(+) and F(-) are higher than that of
F(mean) by a factor of about sqrt(2). R factors will always be higher
for unmerged data because averaging always reduces the uncertainty.
This means that w
On 12 January 2012 09:57, Dirk Kostrewa wrote:
> That doesn't sound wrong to me: the flexible parts are at different relative
> positions in the unit cells and thus their "partial-structure scattering
> waves" do not have a constant phase relation to each other, i.e., they don't
> give a coherent
> We don't see any change of frequency (or wavelength) in the majority
> of the scattering from disordered regions so it's Rayleigh (coherent)
> scattering. There will be a small amount of Compton (incoherent)
> scattering resulting from the ionisation events which are responsible
> for radiation
On 12 January 2012 10:33, Dirk Kostrewa wrote:
> My understanding of coherence is a constant phase relation between waves.
Correct. For a perfect crystal all the unit cells are identical so
they scatter in phase
and this gives rise to the interference effect we see as Bragg spots,
as you say ari
On 12 January 2012 11:25, Dirk Kostrewa wrote:
> I'm not a physicist - but isn't (in)coherence also used to describe the
> property of sources of electromagnetic waves with constant wavelength? For
> instance, an incoherent sodium vapour light source (only looking at one
> emission band) compared
On 12 January 2012 13:02, Weiergräber, Oliver H.
wrote:
> I think the problem is related to the term "coherence" being used to describe
> both the type of *radiation* and the mode of *scattering*.
> When talking about (xray) radiation, it denotes the phase relationship
> between photons, and the
Perhaps I could chime in with a bit of history as I understand it.
The term 'dispersion' in optics, as everyone who knows their history
is aware of, refers to the classic experiment by Sir Isaac Newton at
Trinity College here in Cambridge where he observed white light being
split up ('dispersed')
On 24 January 2012 14:19, David Schuller wrote:
> On 01/24/12 00:41, Bart Hazes wrote:
> www.cs.siue.edu/~astefik/papers/StefikPlateau2011.pdf
>
> An Empirical Comparison of the Accuracy Rates of Novices using the Quorum,
> Perl, and Randomo Programming Languages
> A. Stefik, S. Siebert, M. Stefik
On 24 January 2012 15:23, Greg Costakes wrote:
> It would seem that you have a large model bias. Rule of thumb is to keep
> R/Rfree within 5% of each other. If you find that the numbers
> are separating during refinement you need to reduce the weighting factor
> (dont use automatic) during refinem
On 24 January 2012 08:59, Tim Gruene wrote:
> [flame=;-)]
> P.S.: don't use python. It's a nightmare language, sloppy, it forces you
> to format the code in a specific way rather than your own way and ...
> [/flame]
I'm inclined to go along with you there: the main reason I've put off
learning P
on of the classic prism experiment. You will
> also find an apple tree in the garden, but that is another story..
>
> Peter
>
> PS this is my special ccp4bb email account, it doesn't always get the
> attention it deserves.
>
>
> On 19 January 2012 17:50, Ian T
Jacob, here's my (personal) take on this:
The data quality metrics that everyone uses clearly fall into 2
classes: 'consistency' metrics, i.e. Rmerge/meas/pim and CC(1/2) which
measure how well redundant observations agree, and signal/noise ratio
metrics, i.e. mean(I/sigma) and completeness, which
On 31 January 2012 02:30, Jens Kaiser wrote:
> Hi all,
> we encountered an odd behaviour of REINDEX.
>
> Snip form logfile:
>
> Data line--- reindex HKL (h+l)/2, -k, (h-l)/2
> Data line--- end
>
> Reflections will be reindexed, and unit cell recalculated
>
> Reindexing transformation:
>
Eleanor
Maybe the interpreter should at least throw an error if it encounters
a character (such as a bracket) that it can't interpret, as Jens
implied.
Cheers
-- Ian
On 31 January 2012 10:16, Eleanor Dodson wrote:
> Sorry, but it is a pain writing interpreters - at least it was in Fortran!
>
Reading the H.R.3699 bill as put forward
(http://thomas.loc.gov/cgi-bin/bdquery/z?d112:HR03699:@@@L&summ2=m&;)
it seems to be about prohibiting US federal agencies from having
policies which permit, authorise or require authors' assent to break
the law of copyright in respect of published journal a
llowed by open
>> access.
>>
>> It is, unfortunately, a standard ploy in current American politics to
>> make a
>> law which does something likely to be very unpopular and very unreasonable
>> sound like it is a law doing something quite different.
>>
>
> Can non-US based scientists sign the petition, btw?
Well there's nothing to stop you! It asks for your zip code, but I
just left it blank and it accepted it.
Cheers
-- Ian
is petition? You need a Whitehouse.gov account
> and in order to register you have to provide a U.S. (I presume) zipcode.
>
>
> At 15:37 16-02-2012, Ian Tickle wrote:
>>
>> Dear Herbert
>>
>> Thanks for your detailed explanation. I had missed the important
Francis,
It's very easy to spot a 2-fold rotation or screw because the matrix
must be symmetric (or nearly so)**. Your matrix very obviously is not
(i,e, A12 ne A21, A13 ne A31 etc).
** Proof:
A rotation matrix is orthogonal, which implies inverse = transpose: A^-1 = A~.
A 2-fold rotation is
> (*) ADP = Atomic Displacement Parameters
or "anisotropic displacement parameters"?
See http://ww1.iucr.org/comm/cnom/adp/finrepone/finrepone.html
Section 1.5 Comments about terminology
Cheers
-- Ian
> I'm aware of this document. Personally I prefer "ADP = Atomic Displacement
> Parameters" over anything ele, because, given that Atomic Displacement
> Parameters can be parameterized in many different ways, it makes it easier
> to operate with such terms like:
>
> - isotropic Atomic Displacement P
On 2 March 2012 18:01, Jacob Keller wrote:
> Can't there be a "group of atoms?"
For sure, but doesn't a given parameter either apply to a single atom
or to a group of atoms?
Cheers
-- Ian
> Pavel’s statement is likely a bit of an exaggeration, but he has a valid
> (yet hard to prove point). The default in CCP4i was (and is?) to use
> hydrogens only if present in the input file. This is IMO not a safe default.
I agree: what I find confusing here is that the current CCP4i default
is
matthews_coef ?
-- Ian
On 12 March 2012 17:35, james09 pruza wrote:
>
>
>
>> Dear CCP4bbers,
>>
>> Is there any tool to calculate the Matthews coefficient from a
>> crystallographic model of RNA-protein complex?
>>
>> Thanking you.
>> James.
>
>
... or rwcontents ?
-- Ian
On 12 March 2012 17:35, james09 pruza wrote:
>
>
>
>> Dear CCP4bbers,
>>
>> Is there any tool to calculate the Matthews coefficient from a
>> crystallographic model of RNA-protein complex?
>>
>> Thanking you.
>> James.
>
>
Hi Chris
I would say there's something very wrong if you're seeing -6 sigma
difference peaks at O atoms. I don't see how this can be explained by
radiation damage. I for one have never seen that before in a
structure where there weren't other obvious issues (or maybe I just
haven't looked hard e
PS you say the model is complete, but just as important how complete
is (are?) the data.
-- Ian
On 4 April 2012 16:16, Chris Meier wrote:
> Dear all,
> I am refining the X-ray structure of a protein:
> Data to ~2A were collected at a latest-generation synchrotron.
> The 2fo-Fc maps are crisp, th
The PNAS paper you refer to talks about a "loss of definition" of
exposed carboxyl O atoms, i.e. an increase in B factor, but presumably
if this is modelled properly then it shouldn't leave a big hole in the
difference map. After all, the paper is not claiming that C-O bonds
are broken, only that
> I do not know whether this has recently been changed, but the license for
> icc-produced executables used to be rather restrictive. If I remember
> correctly, you were not allowed to distribute the binaries, full stop.
Nicholas, this restriction applies (and has always applied) only to
Intel's '
> That's right. With a cost of $9,997.00 for a 3-years/2-seats academic
> license,
> I couldn't have been talking for anything else ... :-)))
Hi Nicholas
That sounds like way more than it should be, in fact it sounds like
you've been quoted the cost of the commercial licence and then some!
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