ference between R and Rfree.
>
>Is there a criteria or special range of choosing weighing term? Is
> weighing term 0.1 too small? I read the references by Ian Tickle (Acta
> Cryst D, 1998 and 2000)on R and Rfree ratio, those helped a lot but I
> still do not know the key of weig
Bernhard
Refmac doesn't specify a target value for the chiral volume, it just
specifies 'positive' or 'negative'. It presumably uses the chiral
volume computed from the input co-ords as the target, so this is updated
as the refinement proceeds. I guess the goal isn't to restrain the
geometry to
Hi Bernhard
Oh dear we're getting into naming issues again!! I'm not clear what's the
distinction you're making between 'A Rice function' and 'THE Rice function'
since my understanding was that there was only one form of Rice distribution,
i.e. the one defined here: http://en.wikipedia.org/wik
Hi Thiyagarajan
I doubt that what you want can be done easily, if only because of the problem
that a mouse click returns only 2-D co-ords (x,y) whereas of course you need
the 3-D co-ords (i.e. also z) to identify a point in the map.
There is a way however: simply vary the contour level until th
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Eleanor Dodson
> Sent: 23 April 2009 15:59
> To: Kumar
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] Twinning or not?
>
> Look at the moment plots after scalepack2mtz; if thes
Sorry I don't have instant access to Acta A here so can't comment in the
light of the Flack & Shmueli paper. But it seems to me that Kevin's
point is still valid, regardless of whether or not the anomalously
scattering atoms have different ADPs from the average or not. I agree
that this would hav
Dear George
On the contrary, it's being used, it's just that it's rare for something
to go wrong and the documentation is very clear, so there's very little
cause for complaint!
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
O
Hi Pat
I concur with George, we routinely refine together the group B factor
and occupancy of our ligands and frequently see significant deviations
of the group occupancy from the starting value even if it is highly
correlated with the group B factor (the significance test takes account
of the cor
The other possibility of course is that the data is good, that this is
an accurate experimental result and there really is a void, or at least
a cavity where the mean bulk density is lower than in bulk water. One
way to test the void theory would be to fill the cavity with O atoms of
zero (or very
Sorry found it:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1853337
... and it's Brian Matthews not Mathews.
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Ian Tickle
> Sent: 02 June 200
Ethan - that's odd it works for me (CCP4 6.1.0) unless of course it got
broken recently in 6.1.1:
First an extract from the mtz2various log file:
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
70.3025 68.7834 93.7125 90. 94.1913 90.
* Resolution
them! I2 is merely an
alternative setting of space group no _5_.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Ian Tickle
> Sent: 09 June 2009 10:46
> To: Ethan Merritt; CCP4BB@jiscmail.ac.uk; Ph
> -Original Message-
> From: Ethan Merritt [mailto:merr...@u.washington.edu]
> Sent: 11 June 2009 00:35
> To: Ian Tickle
> Cc: CCP4BB@jiscmail.ac.uk; Phil Evans
> Subject: Re: mtz2various is broken [ was: Another pointless question ]
>
> On Tuesday 09 June 2009 0
ng/naming
convention, shown under 'number' and 'symbol xHM' in syminfo.lib,
because in ITC(A) the name takes precedence over the number. So there
the number should be converted to '5', and of course in PDB files only
the ITC(A) name is used.
Cheers
-- Ian
> -Or
ay be a few programs which might be
able
> to get the wrong spacegroup from an inconsistent file.
>
>
> Ethan Merritt wrote:
> > On Thursday 11 June 2009, Ian Tickle wrote:
> >>> -Original Message-
> >>> From: Ethan Merritt [mailto:merr...@u.washi
r symbol would not
> affect
> > most programs in any way.
> >
> > It is possible of course that there is a way to access the file
symbol
> or
> > number, in which case there may be a few programs which might be
able to
> get
> > the wrong spacegroup from an incons
5 read from header and translated to 'C 1 2 1', and SG name in
header = 'I 1 2 1' is ignored.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Ian Tickle
> Sent: 11 June 2009 17:28
&
Hi Martyn
Since seeing Ethan's last posting I guessed immediately, following on
from what Kevin had said earlier, that the program in Ethan's sequence
which made the change from SG #4005 to #5 in the MTZ header (and my
tests confirm this) is ctruncate; this behaviour presumably is a feature
of the
> -Original Message-
> From: Winn, MD (Martyn) [mailto:martyn.w...@stfc.ac.uk]
> Sent: 12 June 2009 23:31
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: RE: [ccp4bb] mtz2various is broken [ was: Another pointless
> question ]
>
>
> I didn&#x
Hi Jeffrey
Re-indexing this in the conventional setting (i.e. beta nearest to 90 -
for reasons no-one has yet been able to explain to me the standard d.p.
programs do not make this choice automatically!) gives you space group
I2 with cell:
a=58.1 b=95.8 c=76.67 beta=90.24
With beta now so clo
Hi Douglas
Do you have some references with examples of this technique? In my
experience this is a difficult experiment to perform routinely except in
a few special cases. The first problem is that soaking the ligand can
easily induce significant cell dimension changes, which if large enough
cau
The SIGMAA program has since it was written in the 80's (mainly by Randy
of course, but also in part by Eleanor I believe?) used only 1 phase
column (= PHIC) for the case where the phases of FWT & DELFWT are equal
to PHIC: obviously if they are unequal (e.g. as a result of phase
combination) then a
But I thought what you wanted was to reconstruct the diffraction pattern
(i.e. streaks, TDS, ice rings, zingers, warts & all) as a
pseudo-precession image, not just display a representation of the
integrated intensities. That surely would be much more useful, then one
could see whether the apparen
I'm not clear what is the reasoning here behind using a low res cutoff for the
SRF (i.e. lower than the data limit). It seems to me that using all valid data
available can only increase the signal/noise ratio, and omitting good data can
only have a deleterious effect (as will any kind of data i
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Artem Evdokimov
> Sent: 20 July 2009 03:12
> To: 'Junyu Xiao'; CCP4BB@jiscmail.ac.uk
> Subject: RE: [ccp4bb] Density for pyrophosphate?
> Incidentally, if you compress the images yo
> Sent: 20 July 2009 10:35
> To: Ian Tickle
> Subject: Re: [ccp4bb] Density for pyrophosphate?
>
> Dear Ian,
> I got it only once, fortunately, so perhaps the multiplication was the
> fault of a server at your end...
> Mark
>
>
> Mark J. van Raaij
> Dpto de Bi
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Francis E Reyes
> Sent: 21 July 2009 22:22
> To: ccp4bb@jiscmail.ac.uk
> Subject: Self Rotation map in R32?
>
> Hi all
>
> I'm trying to understand why there is a peak that is perp
This nicely illustrates the danger of using too low resolution data to
compute the SRF (I'm referring to an earlier BB discussion on this
subject, where it was suggested to cut out the high resolution data,
against, it seems to me, all rationale). You should be using as high
resolution valid data
age-
> From: owner-ccp...@jiscmail.ac.uk
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Francis E Reyes
> Sent: 22 July 2009 13:51
> To: Ian Tickle; Francis E Reyes
> Cc: CCP4 bulletin board
> Subject: RE: [ccp4bb] Self Rotation map in R32?
>
> >This nicely illustrat
Wikipedia is your friend!
Dispersion is defined as the change in phase velocity with wavelength
(or wave number, frequency etc), see here:
http://en.wikipedia.org/wiki/Dispersion_relation .
The phase velocity is directly related to the refractive index:
http://en.wikipedia.org/wiki/Refractive_ind
ith SHELXD
> and refined it with SHELXE. Than incorporate the coordiantes
> in PHASER EP where I also incorporate the MR structure also.
> This give out a pdb file with another atom set where some of
> occupancies greater than 1.
>
> I was just wondering that how th
All, I know Clemens Vonrhein raised a similar question about the HIS
restraint target values & SUs in the standard library some years ago.
The values currently in use appear to be the Engh & Huber (1991) ones
for the doubly-protonated (+1 charge) imidazole side-chain, so I have 4
questions:
1) Sho
os...@cmbi.ru.nl [mailto:rjoos...@cmbi.ru.nl]
> Sent: 28 July 2009 11:08
> To: Ian Tickle
> Cc: ccp4bb@jiscmail.ac.uk
> Subject: Re: [ccp4bb] HIS restraint target values & SUs.
>
> Hi Ian,
>
> > All, I know Clemens Vonrhein raised a similar question about the HIS
&g
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Pavel Afonine
> Sent: 31 July 2009 03:39
> To: Jiamu Du
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] question of extra high B factor
>
> with B~133 you uj is 3.
Hi Kristof
AFAIK there's no attractive H-bond term in Refmac, only a repulsive one,
and even that is probably between the N/O atoms not between the H atoms
themselves, which only 'ride' on their parent atoms (again this is to my
knowledge). This is all related to the fact that H atoms don't scatt
Tim, Garib,
Sorry, maybe I'm missing something here but how does the user specify
that (s)he wants a TRANS link between standard amino-acids (ASN-GLY) in
this case? Isn't that the default? I always thought the answer was to
add a LINK record for those two residues in the PDB file using the
forma
Hi Eugene & Jawahar
Thanks for responding!
> let me take the liberty. Your reading of PDB documentation is
> absolutely correct. PDB format has got 3 types of links: SSBOND,
> LINK and CISPEP. And indeed, residue numbers have no significance
> in the PDB whatsoever. The connectivity is given by S
Hi Eugene
> If I were to deal with your example, I would look into distance
> profile between residues in coordinate section, which then
> gives answer to your question.
OK that's interesting, I hadn't realised that the interatomic distances
played an active role in determining connectivity: I ha
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Adam Ralph
> Sent: 24 August 2009 15:25
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Linux flavour and hard disks
> You also need a swap partition,
> this should be 2 to 3 ti
Phil
I had this same problem a while ago, if you recall. Modern e-mail
clients sending a message in HTML format will almost certainly send it
in 2 parts, the first a version converted to plain text and the second
the original HTML version (and possibly other versions of the same
message). This i
is
> important, but not in this context)
>
> 2. Messages such as Norman's (and others), which seem to come from
> Outlook Express or Exchange Server, specify a font size 3D2 (whatever
> that means) which comes out too small to read, at least for me
>
> The html line is
rom: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Phil Evans
> Sent: 15 September 2009 12:42
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] attachments
>
> On 15 Sep 2009, at 11:24, Ian Tickle wrote:
>
> >
> > Phil
>
> I suppose I also don't understand why people composing html messages
> would select a tiny font size, or is that a function of the Mail
> reader rather than the writer (which would seem to defeat the purpose
> of the writer formatting the message)?
Assuming your mail reader has correctly interpr
> Why do you say that?
> Typing non-ascii text is the same process whether it's wrapped in HTML or
> not.
> Here's your sigma: ∑
My e-mail client only allows me to insert non-ASCII characters into HTML (or
RTF), not plain text: the option to insert symbols is greyed out in plain text
mode. If I
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of William G. Scott
> Sent: 15 September 2009 15:15
> To: Ian Tickle
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] attachments
> jsMath provides a co
Hi Hugh
A data/parameter ratio of 0.5 does seem low even at 3.4 Ang, I would
expect it closer to 1 (say 0.8 to 0.9) depending on the solvent content.
Why is it low - is your completeness low? What matters from the point
of view of what Rfree you should expect, all being well, is the
observation/p
Hi, I beg to disagree with the 'perceived wisdom', including just about
everyone on this BB, but my answer is NO, there should be no bias -
*provided* you do the subsequent refinement properly. First off, Rfree
is useless as any kind of statistical measure of overfitting etc
*unless* the refinemen
hat (at least) I mean. After convergence of refinement
against
> the second data set, both R and Rfree will be then very similar for
the
> two data sets.
>
> Best regards,
>
> Dirk.
>
> Am 24.09.2009 um 11:56 schrieb Ian Tickle:
>
>
> Hi, I beg to disagree w
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Eric Bennett
> Sent: 24 September 2009 13:31
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rfree in similar data set
>
> Ian Tickle wrote:
>
&
> -Original Message-
> From: Dale Tronrud [mailto:det...@uoxray.uoregon.edu]
> Sent: 24 September 2009 17:21
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rfree in similar data set
>While I agree with Ian on the theoretical level, in pract
7;memory' of
fitting to the new data.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Tom Terwilliger
> Sent: 24 September 2009 16:58
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject
"noise" which is being "overfit" in the
> new dataset could be completely independent from that in the old.
> However I think it is generally agreed that there is a component
> of "noise" (in the most general sense, meaning the difference
> between what is ca
-- Ian
> -Original Message-----
> From: Lijun Liu [mailto:li...@uoxray.uoregon.edu]
> Sent: 24 September 2009 19:00
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rfree in similar data set
>
> Sticking to the same test set is a great and practical i
The patent #7504486 you cited actually only covers 'A method of growing
a crystal of a 50S ribosomal subunit from Haloarcula marismortui', i.e.
the crystallisation method for the 50S subunit from this single organism
(from my school Latin I deduce 'haloarcula' = 'small box of salt' and
'marismortui
Hi Sylvia
You didn't make it clear on what basis you think the discrepancy between
R and Rfree is too big, since the Rfree you would expect to get if the
refinement were bias-free depends a lot on a number of factors such as
the resolution, the data completeness, what parameters you are refining,
Hi Sylvia:
> -Original Message-
> From: Sylvia Fanucchi [mailto:sylvia.fanuc...@wits.ac.za]
> Sent: 19 October 2009 15:06
> To: Ian Tickle
> Subject: RE: how to improve Rfree?
>
> Hi Ian
>
> Yes, sorry, admittedly this is the first time I'm doing th
> (& while I'm at it, freeR has nothing to do with model bias (which is
> largely imaginary anyway, only a problem with low resolution molecular
> replacement))
>
> Phil
Phil, I understand what you're saying but 'model bias' in this context
has a wider meaning than just failing to rebuild the cha
> If you have non-crystallographic symmetry the effects are uncertain,
but
> in many cases this too gives you a lower than expected FreeR value,
and
> again, that doesnt mean you have a better structure..
>
> In general the difference in R and Rfree should be correlated with the
> resolution, but
> Bias is defined as 'difference from expectation', so the isotropic
model
> is almost certainly biased, as reflected in the higher-than-expected
> Rwork & Rfree.
Phil, sorry in my rush to go home I explained that badly: bias is
defined as 'difference between the expected and true values'. In thi
> -Original Message-
> From: Vellieux Frederic [mailto:frederic.velli...@ibs.fr]
> Sent: 19 October 2009 19:31
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] how to improve Rfree?
>
> Hi Ian (& ccp4bb'ers),
>
> NCS ties
Hi Jacob
That doesn't surprise me at all, though the example you heard is
probably towards the extreme end of what we've seen. We have seen
individual cell parameter changes up to 10% on soaking/freezing which
could easily add up to 20-30% change in cell volume. One problem with
freezing is that
All - we're having a problem with Refmac (version 5.5.0102) in CCP4
6.1.2 that I compiled from source using ifort v11.0 on Centos 4.6. When
I refine a structure with a HIS in alternate conformations (all atoms
except N, C & O doubled up) it completely destroys the sidechains of
both copies. Same
Huw, I guess you're referring to my original posting of this problem.
When I used binary version 5.5.0109 (compiled by gfortran I assume)
downloaded from Garib's site as he suggested instead of the 5.5.0102
version I compiled myself using ifort (because gfortran had given
trouble in the past), the
Yes higher R factors is the usual reason people don't like I-based
refinement!
Anyway, refining against Is doesn't solve the problem, it only postpones
it: you still need the Fs for maps! (though errors in Fs may be less
critical then).
-- Ian
On 20 June 2013 17:20, Dale Tronrud wrote:
>I
suggestion ...
> >
> > D
> >
> >
> >
> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Ian Tickle
> > Sent: 20 June 2013 17:34
> > To: ccp4bb
> > Subject: Re: [ccp4bb] ctruncate bug?
> >
> > Yes higher R factors is th
the decay of scattering background (kind of Wilson
> plot of background scattering) to flat out the background and push all the
> Is to positive values?
> >>>
> >>> More of a question rather than a suggestion ...
> >>>
> >>> D
> >>>
> >
On 20 June 2013 20:46, Douglas Theobald wrote:
> Well, I tend to think Ian is probably right, that doing things the
> "proper" way (vs French-Wilson) will not make much of a difference in the
> end.
>
> Nevertheless, I don't think refining against the (possibly negative)
> intensities is a good s
On 21 June 2013 13:36, Ed Pozharski wrote:
> Replacing Iobs with E(J) is not only unnecessary, it's ill-advised as it
> will distort intensity statistics. For example, let's say you have
> translational NCS aligned with crystallographic axes, and hence some set of
> reflections is systematically
On 21 June 2013 17:10, Douglas Theobald wrote:
> Yes there is. The only way you can get a negative estimate is to make
> unphysical assumptions. Namely, the estimate Ispot-Iback=Iobs assumes that
> both the true value of I and the background noise come from a Gaussian
> distribution that is all
On 21 June 2013 19:45, Douglas Theobald wrote:
>
> The current way of doing things is summarized by Ed's equation:
> Ispot-Iback=Iobs. Here Ispot is the # of counts in the spot (the area
> encompassing the predicted reflection), and Iback is # of counts in the
> background (usu. some area around
On 22 June 2013 18:04, Douglas Theobald wrote:
> Ian, I really do think we are almost saying the same thing. Let me try to
> clarify.
>
I agree, but still only "almost"!
> --- but in truth the Poisson model does not account for other physical
> sources of error that arise from real crystals
On 22 June 2013 19:39, Douglas Theobald wrote:
>
> So I'm no detector expert by any means, but I have been assured by those
> who are that there are non-Poissonian sources of noise --- I believe mostly
> in the readout, when photon counts get amplified. Of course this will
> depend on the exact
Last time I checked pdbset doesn't renumber the LINK, CISPEP, SSBOND
records at the same time (but maybe it was fixed).
-- Ian
On 26 June 2013 07:41, Francois Berenger wrote:
> I think pdbset from CCP4 can renumber a PDB and hence get rid of the uggly
> insertion codes.
>
>
> On 06/26/2013 03:
On 21 June 2013 13:36, Ed Pozharski wrote:
> Replacing Iobs with E(J) is not only unnecessary, it's ill-advised as it
will distort intensity statistics.
On 21 June 2013 18:40, Ed Pozharski wrote:
> I think this is exactly what I was trying to emphasize, that applying
some conversion to raw int
Ed, sorry, not sure what happened to the 1st attachment, it seems to have
vanished!
Cheers
-- Ian
<>
On 29 June 2013 01:13, Douglas Theobald wrote:
> Just because the detectors spit out positive numbers (unsigned ints) does
> not mean that those values are Poisson distributed. As I understand it,
> the readout can introduce non-Poisson noise, which is usually modeled as
> Gaussian.
>
OK but po
On 8 July 2013 18:29, Douglas Theobald wrote:
> That's all very interesting --- do you have a good ref for TDS where I
> can read up on the theory/practice? My protein xtallography books say
> even less than S&J about TDS. Anyway, this appears to be a problem
> beyond the scope of this present
On 22 August 2013 07:54, James Holton wrote:
> Well, yes, but that's something of an anachronism. Technically, a
> "Miller index" of h,k,l can only be a triplet of prime numbers (Miller, W.
> (1839). A treatise on crystallography. For J. & JJ Deighton.). This is
> because Miller was trying to
On 1 September 2013 11:31, Frank von Delft wrote:
>
> 2.
> I'm struck by how small the improvements in R/Rfree are in Diederichs &
> Karplus (ActaD 2013, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689524/);
> the authors don't discuss it, but what's current thinking on how to
> estimate the expe
On 1 September 2013 11:31, Frank von Delft wrote:
>
>> 2.
>> I'm struck by how small the improvements in R/Rfree are in Diederichs &
>> Karplus (ActaD 2013, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689524/);
>> the authors don't discuss it, but what's current thinking on how to
>> estimate the
Hi Maggie
echo symm P212121 | mtzutils HKLIN in.mtz HKLOUT out.mtz
should do the trick.
Cheers
-- Ian
On 6 November 2013 18:13, MAGGIE wrote:
> Hi,
>
> I have a structure which should have space group P212121, but it has been
> processed to P21212. It can not be solved and refined.
I agree completely with Tim: I use 'man' (or 'info' for gfortran & the
like) all the time - but then I'm a die-hard command-liner/shell-scripter
who never uses ccp4i! I haven't got around to installing 6.4 yet but if &
when I do & I find the man pages missing as Tim says I'll probably copy
over th
Hi Wenhua
You didn't say what resolution your structure is: that's critical to
deciding how significant is the R-factor difference (or more strictly the
ratio). There are other factors such as solvent content: generally
anything which affects the obs/param ratio (such as NCS restraints) will
also
Hello All, I'd like to get your views on some changes I'm proposing to make
to the TRUNCATE source code. IMO there are some issues with the way
TRUNCATE does its statistical analyses which need to be fixed. This
probably doesn't affect the MTZ file that comes out of it but it will
affect the stat
Robbie
That sounds more like a programming error: the issues I've identified are
purely numerical and won't affect the program flow.
Cheers
-- Ian
On 4 December 2013 09:23, Robbie Joosten wrote:
> Hi Ian,
>
>
> > This probably doesn't affect the MTZ file that comes out of it
> > but it will
Dear Herman
TLSANL doesn't need a TLS file, it will read the PDB header if you don't
give it one. Sorry if that's not explained in the documentation. It was a
feature I added recently.
Cheers
-- Ian
On 11 December 2013 10:59, wrote:
> Dear bulletin board,
>
> I recently submitted a coordi
All, I'm having problems refining a structure with an N-terminal acetylated
MET residue. I'm trying it with both Refmac & Buster. Buster works fine &
gives perfect planar geometry for the ACE-MET linkage. Refmac gives a
pyramidal acetyl group after refinement which to my eyes is wrong (sp2 C
ato
e for insertion in COOT-check this file
>
> P.S.: I hope you are still able to understand my runglish
> 14.02.2014 02:57, Ian Tickle пишет:
>
>
>> All, I'm having problems refining a structure with an N-terminal
>> acetylated MET residue. I'm trying it with both R
ld like to know.
>
> Regards
> Garib
>
>
> On 13 Feb 2014, at 22:57, Ian Tickle wrote:
>
>
> All, I'm having problems refining a structure with an N-terminal
> acetylated MET residue. I'm trying it with both Refmac & Buster. Buster
> works fine & giv
On 27 March 2014 14:23, Jarrod Mousa wrote:
> Using I/sigI > 3 with completeness above 0.85, the estimated useful
> Resolution Range of this data is 17.964A to 8.982A
>
Hi, I would imagine that the message above has something to do with it.
Cheers
-- Ian
Hi Edward
As far as Eulerian rotations go, in the 'Crowther' description the 2nd
rotation can occur either about the new (rotated) Y axis or about the old
(unrotated) Y axis, and similarly for the 3rd rotation about the new or old
Z. Obviously the same thing applies to polar angles since they can
olecule. My view would be to say
> the first and final rotation are rotating about the perpendicular to the
> screen which we have kept equal to the z axis, and it is the same z axis.
>
> Ed
>
> >>> Ian Tickle 03/29/14 1:39 PM >>>
>
> Hi Edward
>
>
will be about y, will leave the y coordinates
> unchanged, and we see rotation about the vertical axis. Final rotation
> about z is in the plane of the screen again, although this represents
> rotation about a different axis of the molecule. My view would be to say
> the first and final
Ed,
OK, I need to think about this more when I have time, but at this point
> I think it is a semantic difference- For me the first and last rotation are
> about the same Z axis because as you say they are both around the screen Z
> axis
> and both operators look like cos,sin, 0, -sin, cos, 0, 0
Ed,
> I think we are saying the same thing here. When I say the axes are kept
fixed, I mean they are the screen axes. When you say "new axis" you do not
mean that the axis has been rotated, but that it passes through the
molecule differently. Or maybe not . . .
No I mean exactly that. What I'm s
On 1 April 2014 00:12, Edward A. Berry wrote:
> I need to work on something else now, but when i get time I will go
> through Ian's derivation and see how it is in fact tractable.
>
I should point out that it's not my derivation. This proof was given to me
by Tilman Shirmer. For the original
On 1 April 2014 00:12, Edward A. Berry wrote:
> Yes of course, but if you start from the left you are not (at least not
> obviously)
> "first rotating the coordinates by alpha about z"; you are rotating the
> columns
> of the second matrix. And in the second multiplication you are not
> rotating
On 2 April 2014 12:49, Tim Gruene wrote:
> P.S.: complex numbers together with the operation '+' defined in the
> canonical way fulfill the axioms of a vector space, hence complex
> number are vectors. If you also take the operation '*' into account,
> defined in the canonical way, (C, +, *) fulf
On 2 April 2014 13:39, Ian Tickle wrote:
> scalar satisfies other axioms (e.g. multiplication & addition) that a
> vector doesn't.
Sorry typo:
A scalar satisfies other axioms (e.g. multiplication & _division_) that a
vector doesn't.
I.
Hi Bernhard
My understanding, gleaned from ITC-A and ITC-B is that the 65 space groups
listed here: http://www.ccp4.ac.uk/dist/html/alternate_origins.html that I
assume you are referring to, are "enantiomorphic", which is defined as "not
possessing improper rotations" (see
http://pd.chem.ucl.ac.uk
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