Depending on the Space (Laue) group, there may be alternative indexing
possibilities which will be sorted out in Pointless - did you run that program?
I would recommend using the ccp4i task Symmetry, Scale, Merge (Aimless) which
uses Aimless instead of Scala - Aimless may be a bit more robust
We know that our scaling models do not completely describe and compensate for
all systematic errors, for various reasons including radiation damage (which is
hard to model). This can be seen by scaling together data collected about
different axes, where typically the merging statistics between
If you want to import integrated files from XDS into Pointless and Aimless, you
should use Pointless to do the conversion rather than the older program Combat.
This is what is done if you use the ccp4i interface task Symmetry, Scale,
Merge (Aimless)
Combat wrongly fills in the FRACTIONCALC
In response I felt I had to post the low-tech version (not mine)PhilOn 16 Jul 2013, at 11:57, Edward Lowe edward.l...@bioch.ox.ac.uk wrote:At Elspeth's request, here's a link to a picture of the rack we use fordrying out shipping
I hope that some [X]Emacs expert can rewrite Charlie Bond's wonderful pdb-mode
to work with mmCIF files (or at least the coordinate bits)
… for exactly the reasons Phil Jeffrey points out
Phil
On 8 Aug 2013, at 00:54, Jeffrey, Philip D. pjeff...@princeton.edu wrote:
Nat Echols wrote:
(or at least
in my current copy, updated a few weeks ago). So there is an inconsistency -
no doubt this will be sorted out shortly.
If you want a 64-bit build of Pointless for OSX then see Phil Evans' ftp
site -
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre
Use the most recent version
multiplicity = 1.0?
On 14 Aug 2013, at 15:59, Yafang Chen yafangche...@gmail.com wrote:
Dear All,
I recently processed a dataset, in which I/sigmaI of the last shell is 2.3,
while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0?
The completeness is 100 (100). Thank
The question you should ask yourself is why would omitting data improve my
model?
Phil
On 27 Aug 2013, at 02:49, Emily Golden 10417...@student.uwa.edu.au wrote:
Hi All,
I have collected diffraction images to 1 Angstrom resolution to the edge of
the detector and 0.9A to the corner.I
7:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution, R factors and data quality
Hi all,
does this not again bring up the still prevailing adherence to R factors and
not a shift to correlation coefficients ( CC1/2 and CC*) ? (as Dr. Phil
Evans has indicated).?
The way we
criterion
( which I guess is done to be on the safe side- Dr. Phil Evans can explain if
there are other or an entirely different reason to it! ). But if we want to
squeeze the most from our data-set, I guess we need to push a bit further
sometimes :)
On Wed, Aug 28, 2013 at 9:21 AM
As long as the .sca file is scaled but unmerged, then one way is
pointless -copy scain denzo.sca hklout denzo.mtz
aimless hklin denzo.mtz EOF
scales constant
onlymerge
EOF
Phil
On 18 Sep 2013, at 11:21, Francesco Angelucci francesco.angelu...@uniroma1.it
wrote:
Dear All,
I am wondering
As a novice looking at mmCIF from a developers point of view, for reflection
data, the complication is not so much tokenising (parsing), but what items to
write or to expect to read. For example as far as I can see an observed
intensity may be encoded in a reflection loop (merged or unmerged)
that they have to deal with in this
field. My experience suggests that this is an important practical issue with
real-world ramifications, and it is worthwhile devoting some effort to it.
Regards,
Peter.
On Wed, 18 Sep 2013, Phil Evans wrote:
Date: Wed, 18 Sep 2013 13:38:07 +0100
From: Phil Evans
that this is an important practical issue with
real-world ramifications, and it is worthwhile devoting some effort to it.
Regards,
Peter.
On Wed, 18 Sep 2013, Phil Evans wrote:
Date: Wed, 18 Sep 2013 13:38:07 +0100
From: Phil Evans p...@mrc-lmb.cam.ac.uk
To: CCP4BB@JISCMAIL.AC.UK
. They are for different purposes and, therefore, could
differ from each other -- Eugene
On 19 Sep 2013, at 10:45, Phil Evans wrote:
Do you really want to read the whole of a long reflection loop into memory
rather than parsing it one line at a time (which should be possible once you
have
Please explain how you think that cutting back the resolution will improve your
model
Phil
On 10 Oct 2013, at 21:57, Yafang Chen yafangche...@gmail.com wrote:
Hi All,
I have a structure at 2.45A which has been well refined. However, since the
R-merge at the last shell is above 1 (although
That won't work. Aimless expects intensities not Fs. I would think you could do
it with sftools
Phil
On 25 Oct 2013, at 09:54, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
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Hash: SHA1
Dear Rojan,
I would try aimless with the option 'onlymerge'.
Best,
I had this problem last week but it seems to have been solved by reinstalling
the ccp4 6.4.0 package today, slightly updated I believe
There was message from Eugene Krissinel which may be relevant to this
Phil
On 28 Oct 2013, at 16:00, Dmitry Rodionov d.rodio...@gmail.com wrote:
Good day!
It should be printed at the end of the log file
P.R.Evans and G.N.Murshudov, 'How good are my data and what is the
resolution?' Acta Cryst. D69, 1204-1214 (2013).
Phil
On 8 Nov 2013, at 11:35, Zheng Zhou zhengzho...@gmail.com wrote:
Dear all
I am also looking for aimless reference.
Always deprecated, hopefully never common!
On 14 Nov 2013, at 11:27, Mark J van Raaij mjvanra...@cnb.csic.es wrote:
It used to be common to only include reflections for which I x sigma(I) in
refinement, with x often being 3.
However, nowadays this is not considered good practise, as
AFAICS the .doc files look as if they were auto-generated from the .html files
in 6.3.0. Certainly the only documentation I have written for Pointless and
Aimless is in html
Phil
On 15 Nov 2013, at 14:33, Edward A. Berry ber...@upstate.edu wrote:
(assuming of course the .doc files aren't
I've generally found that adding lines to the standard table works, and they
are not removed by editors
On 19 Nov 2013, at 09:32, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
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Hash: SHA1
Dear Graeme,
On 11/19/2013 09:02 AM, Graeme Winter wrote:
[...]
Dear Jens
I'm surprised by this as Scala hasn't changed for quite a long time, as it is
now now superseded by Aimless. However, I haven't implemented a reference
dataset in Aimless since in the end I decided that it wasn't very useful, so if
you find it useful then you will indeed need to use
Indeed that is a bug. I've never tried that combination before. I'll fix it
Phil
On 16 Jan 2014, at 20:32, wtempel wtem...@gmail.com wrote:
Hello,
using merged scalepack intensities and a reference MTZ file as inputs, I
would like to prepare an MTZ of scalepack intensities reindexed so that
I/sigmaI
On 12 Feb 2014, at 11:43, Cai Qixu caiq...@gmail.com wrote:
Dear all,
Does the I/sigmaI in “Table 1” mean for I/sigmaI or I/sigmaI ?
Thanks for your answer.
Best wishes,
Qixu Cai
If you assigns them to different datasets in Pointless, then Aimless will give
you the cross-dataset correlations. By default it will scale them to together
first, but you can skip that if you want
It might not scale well to a large number of files (OK up to about 10 I guess)
Phil
On 14 Mar
The polar angles ϕ, ω define the direction of an axis about which a rotation by
angle κ occurs, i.e. a single rotation around a defined axis. This is different
from Eulerian angles which define 3 successive rotations around principal axes
On 27 Mar 2014, at 06:11, Qixu Cai caiq...@gmail.com
Just tested with a clean binary install on a Mac (running 10.8), and it works
for me
Phil
On 8 Apr 2014, at 15:19, Björn Kauppi bjorn.kau...@karobio.se wrote:
Hi
I run latest CCP4 as of today, 6.4.0 update 12 and CCP4i 2.2.1
When trying to run pointless/aimless from the interface the
Was there a reason that you turned off the scaling in Aimless (onlymerge)? If
the data have come from Mosflm, this is definitely wrong - the result is that
(among other things) you have negative CCanom values which is unusual to say
the least
Just run it with the default options, that's
I2 and C2 are different settings of the same group. The official IUCr
convention is to use the one which gives the beta angle closer to 90 degrees.
As far as I know all programs should now be able to use the I2 setting, but if
it worries you, you can reindex to C2
Phil
On 21 May 2014, at
Surely Refmac or any other program should honour the symmetry operators in the
MTZ file - that's why they are there!
Phil
On 23 May 2014, at 12:34, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:
Someone here has seen his Rfactors leap from 18% to 42% and was naturally
distressed!
We
OK I guess Pointless is accepting the number as given in the reference file,
rather than changing it.
If Pointless is just determining the space group it does give the correct
(i.e. weird CCP4 convention) number
* Space group = 'P 2 21 21' (number 3018)
I'm not sure how to test this as I
That looks good to me Mean(I/sigma) = 2.0, CC1/2 0.74
See endless discussions on this BB about the uselessness of Rmerge as a
resolution criterion
Phil
On 2 Jun 2014, at 09:27, sreetama das somon_...@yahoo.co.in wrote:
Dear All,
What are reasonable values of Rmerge in the
XDS_ASCII.HKL or scalepack format ('no merge original index') can be read
directly by Pointless which should (I hope) do a better job than COMBAT.
Aimless ( Pointless) assume two reflections are part of the same one if they
have the same true hkl (same ISYM) and adjacent batch numbers (and a
What version of Aimless are you running? I thought I had fixed that bug
Phil
On 13 Jun 2014, at 11:59, Andreas Förster docandr...@gmail.com wrote:
Dear all,
I'm trying to scale/merge mtz files in ccp4
(Pointless/Aimless/ctruncate/Rfree pipeline) and keep getting an
UNHANDLED EXCEPTION:
Do run the data through Pointless before Scala to check the point group.
Try scales constant just to check that things aren't completely hopeless
Phil
On 6 Apr 2012, at 20:29, Yuri Pompeu wrote:
Hi everyone,
Sorry for the newbie type problems, but I am just starting to use ccp4 for
data
I wouldn't recommend this option
Phil
On 6 Apr 2012, at 21:41, Matthew Chu wrote:
Hi all,
Can someone kindly explain what is that match pairs related by inversion of
indices option doing for handling anomalous data? If I have collected the
inverse beam data, does it mean I have to use
On 8 Apr 2012, at 21:18, aaleshin wrote:
What I suggested with respect to the PDB data validation was adding some
additional information that would allow to independently validate such
parameters as the resolution and data quality (catching of model fabrications
would be a byproduct of
and 5A in the third.
Alex
On Apr 9, 2012, at 4:51 AM, Phil Evans wrote:
On 8 Apr 2012, at 21:18, aaleshin wrote:
What I suggested with respect to the PDB data validation was adding some
additional information that would allow to independently validate such
parameters as the resolution
Aimless is a complete rewrite of Scala, but does essentially the same task. I
haven't yet written it up properly, but there is a program document at
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/aimless.html
A rough flow of the program is as follows:-
Read file from eg POINTLESS, sort data if
Yes
Sent from my iPhone
On 6 May 2012, at 11:21, Acoot Brett acootbr...@yahoo.com wrote:
Dear All,
In the crystallography paper table 1, there is Values in parentheses are for
the highest resolution shell. Is this highest resolution shell same as the
OuterShell for the analysis result
SCALA doesn't do anything with the mosaicity, it just reports what was passed
from the integration program.
On 25 May 2012, at 17:12, Ed Pozharski wrote:
I should do more digging, but I hope maybe there is a simple explanation
and someone has seen this before. On some datasets (collected at
NO do NOT invert the hand. If you do you will end up with left-handed helices
etc
The alternative indexing systems all need to preserve the right-handed axis
system imposed by the data integration program (eg k,h,-l)
The ONLY time it is valid to invert the hand is if the indexing/integration
On 29 May 2012, at 15:02, Ian Tickle wrote:
Phil,
On 29 May 2012 14:08, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
NO do NOT invert the hand. If you do you will end up with left-handed
helices etc
Surely not if you take care to also change the signs of the anomalous
differences?
I
Although there is no need for a standard reciprocal asu, it is convenient to
have all your datasets in the same convention when it comes to comparing and
combining different isomorphous datasets (ie to do it once rather than every
time you compare them). It doesn't matter what the standard is
How do you know the point group is 321? What does Pointless tell you if you put
in the unmerged data?
Despite some of the things said earlier (by me!), the possible indexing schemes
in 321 are h,k,l and -h,-k,l
If that doesn't work, it suggests that the point group is a lower symmetry eg P3
As the K D paper points out, as the signal/noise declines at higher
resolution, Rmerge goes up to infinity, so there is no sensible way to set a
limiting value to determine resolution.
That is not to say that Rmerge has no use: as you say it's a reasonably good
metric to plot against image
No they were not useless! I used them
(probably better now with cryo data though)
Phil
On 6 Jun 2012, at 16:02, Dyda wrote:
I suspect that pure MIR (without anomalous) was always a fiction. I doubt
that anyone has ever used it. Heavy atoms always give
an anomalous signal
Phil
I
Just to be clear, the CCP4 data processing programs (SCALA and its replacement
AIMLESS) always give you I+ and I- in the output. The only difference between
anomalous on off is in the outlier rejection, since if you have a large
anomalous signal you don't want to reject as outliers reflections
Personally I'd be happy to share my old datasets if I could find them
Phil
On 3 Jul 2012, at 03:39, Bosch, Juergen wrote:
Dear CCP4 community,
what's the general opinion regarding sharing old published data sets ?
Would you be offended if I asked you for your raw images from say a 5-10 year
Note that neither Aimless nor Scala will do a particularly good job at scaling
data from Denzo or Scalepack, since the output files from Scalepack are missing
essential geometrical information. They work well with data from Mosflm or XDS
(or Saint) (although AFAIK the XDS Saint scaling
An earlier post said the point-group is P2, and these reported cells do not
quote the beta angles: what are these angles?. In the monoclinic system it is
possible to have two closely-similar alternative cells in certain special
cases, and if the crystals have been indexed differently this could
This must be a problem on Windows as it doesn't show up on OSX or Linux, and
this code hasn't changed for a long time, I think
David I guess you will feed this back to me: I don't have any way of testing on
Windows
Anyway, Aimless should be better :-)
Phil
On 4 Aug 2012, at 14:26, David
As Jürgen says why not use imosflm? Incidentally CCP4 6.1.13 is pretty old - I
would recommend updating to 6.3.0
If you REALLY want to convert denzo orientation to the Mosflm convention,
there's an old Fortran program of mine at
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/denzo2mosflm.f
but I
the angle of rotation is kappa = 160.045deg in this case
On 24 Aug 2012, at 04:33, Appu kumar wrote:
Sir one more help plz i have the following matrix which one shall i use to
calculate the angle.
INFO:: coordinates transformed by orthonal matrix:
| -0.6927, -0.7191,0.0564|
|
Note that Scala Aimless always put I+, I- and Imean into the output file,
which then get propagated through [c]truncate. This is irrespective of whether
the Anomalous data flag is switched on: that only affects outlier rejection and
some statistics. Note also that Aimless (recent versions
not god I don't think I wrote that bit!
Phil
On 5 Dec 2012, at 15:06, Ed Pozharski wrote:
Francois,
I did not realize Phil Evans is god (perhaps a minor one as he did not
yet earn a capital G).
I do concur that insertion code is evil. I had to re-refine an old
antibody structure
It is internally consistent, though not necessarily correct
On 7 Dec 2012, at 16:23, Alan Cheung wrote:
Related to this, I've always wondered what CC1/2 values mean for low
resolution. Not being mathematically inclined, I'm sure this is a naive
question, but i'll ask anyway - what does
The Pointless and the Pointless/Aimless tasks in ccp4i will allow multiple
input MTZ (or XDS) files to be combined and scaled together. The combining is
done in the program Pointless
On 11 Dec 2012, at 03:51, Yuri Pompeu wrote:
Thanks for all the suggestions on and off BB.
I used the GUI
… is 20.12.2012
Happy Christmas everyone!
Phil
On Tue, Feb 12, 2013 at 06:52:19PM +0100, Phil Evans wrote:
Ah I'm not sure about that. It may be possible to tell ctruncate not to do
this. Actually if you started with Fs you don't want to truncate the data.
Maybe use old truncate with the notruncate option
Phil
Sent from my iPad
It's nothing to do with Scala! It's something to do with chaining successive
programs in a task I think. I have seen it happen but I can't remember what the
cause is
Phil
On 8 Mar 2013, at 11:49, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote:
(Is it time to change the macabre title of
what happened to all the even l h reflections?
Phil
On 15 Mar 2013, at 15:09, gengxiang zhao gzh...@gmail.com wrote:
Dear CCP4s,
I am looking for more experienced concerns to determine which space group my
crystal is. At present, we take it as P42212 (#94).
HKL is below:
Reference:
Gibbons, S. (1932) Cold Comfort Farm, Longmans, London
On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it
wrote:
Hi everyone,
just a curiosity, why the name aimless for the recent data reduction and
analysis program in CCP4? You know, my students are
Entirely appropriate for data processing!
and Aimless is clearly some sort of optimisation program :-)
Phil
On 2 May 2013, at 11:31, Andreas Förster docandr...@gmail.com wrote:
Occasionally given to losing extremities.
is that a good thing?
Andreas
On 02/05/2013 11:10, Phil Evans
This is not at all critical, as it is only used to put the data on a
_very_ rough absolute scale
... but since a nucleic acid residue is about twice the size of a
typical amino acid, you could say 111
Phil
On 12 Apr 2007, at 12:03, Raymond Yengo wrote:
Hi all,
I am trying to convert
I believe this is a combination of errors in COMBAT (not setting cell
constraint flags correctly) and SCALA (not detecting properly that
they are unset)
I believe that I have fixed the Scala error in my latest version
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/scala_3.2.28.tar.gz
(I hope!)
There
An additional fix of Clemens' made in 3.2.29
ftp://ftp.mrc-lmb.cam.ac.uk/scala_3.2.29.tar.gz
Phil
On 27 Apr 2007, at 10:10, Clemens Vonrhein wrote:
Hi Phil,
these diffs I made to 3.2.27 - seem to fix some other things too.
Cheers
Clemens
On Fri, Apr 27, 2007 at 09:50:16AM +0100, Phil
I always liked Kevin's comments on little-used options in the DM
documentation
Don't use these unless you really know what you are doing. In which
case you'd better have a better idea of what you
are doing than I do.
Phil
On 10 May 2007, at 13:07, Kevin Cowtan wrote:
Miguel Ortiz
I would agree with Clemens that the Scala GUI task generates far too
many keyworded commands, for things which have sensible defaults in
the program.
One problem conundrum for the GUI (because it works by generating a
script without actually running the program) is that the GUI has no
I worry a bit about some of this discussion, in that I wouldn't like
the free-R-factor police to get too powerful. I imagine that many of
us have struggled with datasets which are sub-optimal for all sorts
of reasons (all crystals are multiple/split/twinned; substantial
disordered
Kevin
Does this give the correlation between two (weighted) complex Fs,
which is arguably (ref Bricogne) the best measure, as it corresponds
to the map correlation but as a function of resolution?
Phil
On 28 Aug 2007, at 17:22, Kevin Cowtan wrote:
Yup. cphasematch
It gives unweighted
flame
As an aside, does anyone understand why MSE is not an amino-acid?
Phil
/flame
On 30 Aug 2007, at 15:31, Clemens Vonrhein wrote:
If your PDB file conforms to standard
http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
you could do
% egrep ^CRYST|^SCALE|^ATOM your.pdb
On 31 Aug 2007, at 21:52, Bryan W. Lepore wrote:
[1] is there a way to make pointless read only up to a certain
batch number?
Not at present - I'll add it at some stage, it wouldn't be hard
You can use rebatch to select batches
[2] should pointless compare axial reflections along all
Is there an archive of ccp4-dev? I can't find one
Phil
sortwater (CCP4) will do this
On 3 Oct 2007, at 15:57, Vineet Gaur wrote:
Hi All
i am solving a structure with four molecules in asymmetric unit.
Initially i was refining the structure with four fold NCS, which
now i have removed. i have picked some of the water molecules after
We've had a case recently (unpublished) with 4 molecules in the
asymmetric unit, two self-contained and two domain-swapped
(asymmetrically)
... anything is possible, though in this case the domains are
really separate proteins expressed as an artificial fusion
Phil
On 5 Oct 2007, at
It just picks the first in the list, to store in the output MTZ file,
which can only handle one (92 96)
Phil
On 8 Nov 2007, at 22:26, Bryan W. Lepore wrote:
when pointless (1.2.0) finds enantiomorphic SG's, what is the
criterion for 'Selecting' one over the other?
e.g. i ran pointless
I agree
On 9 Nov 2007, at 13:50, Eleanor Dodson wrote:
As I often say!!! The mtz format should carry point group and
alternate SGs - then be upgraded when youknow the correct SG..
Eleanor
Phil Evans wrote:
It just picks the first in the list, to store in the output MTZ
file, which can
I don't know what this error is, but you might like to know that the
program Pointless can be used as
an alternative to sortmtz, with the bonus that it might help you
determine the spacegroup
You can get it either from our ftp site here
eg
You should certainly try the other P 4x 3 2 space groups (x=1,2,3) in
case the assignment of screw axes is wrong
Phil
On 13 Nov 2007, at 13:17, Kristof Van Hecke wrote:
Dear all,
When running Pointless 1.2.0 (see summary below), I get the cubic
space group P 4 3 2
(mosflm gave P 2 3
is wrong since they have been applied already)
Will this cause anyone problems? I suspect that very few people or
programs are using this file
Phil Evans
From: CCP4 bulletin board on behalf of Phil Evans
Sent: Mon 19/11/2007 5:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unmerged output from Scala
Is anyone using the OUTPUT UNMERGED option in Scala?
This file contains columns called SCALE SIGSCALE which are the
applied scale and its
The maximum likelihood method used in Phaser doesn't use any cut-off
as it doesn't use the Patterson formulation. It might work better for
such an elongated case
Phil
On 28 Nov 2007, at 17:04, Pietro Roversi wrote:
Dear everyone,
is any of the
There is an (possibly) easier way now in pre-release
1) Download install (manually) from the CCP4 pre-release site the
program pointless and the ccp4i task interface
2) Use the Find or Match Laue Group option (under Data Reduction)
to open the interface window to the program Pointless
pointless now does this
Phil
On 11 Jan 2008, at 11:05, Frank von Delft wrote:
There's a way to avoid having to do this - use the ADD sub-
keyword when processing in Mosflm, so that the batch number for
each image data is given an offset; see
Nevertheless, it *is* a right-royal pain in the
I thought that as author of Scala I might put in my 2 penn'th to this
discussion, FWIW
1. I've never been able to find any useful distinction between Rsym
Rmerge, and when filling in the PDBs request for both (undefined by
them and irritatingly restricted to 0.99, at least in Autodep) I
There was a bug in Pointless for XDS reading due to my
misunderstanding of the STARTING_FRAME value, which is fixed in
version 1.2.13, available from
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.2.13.linux (eg)
Otherwise if you send me the file I'll investigate
Phil
On 20 Feb 2008,
That was _supposed_ to say I'm not sure ... !
On 21 Feb 2008, at 21:01, Phil Evans wrote:
On 21 Feb 2008, at 18:24, George M. Sheldrick wrote:
All SHELX programs and XPREP are also indifferent to the asu choice
and to whether the data have been merged or not (even SHELX-76). It
is CCP4
Since there has been mention of putting data from XDS into Pointless,
I should say that I have made yet another (!) fix today for reading
XDS data. It now flags ignores reflections marked as MISFITS in the
XDS file (marked with SD 0). Previous versions included these
reflections which at
As Graeme says, Pointless should sort this out for you, either from
CCP4 pre-release,
or from ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre
Phil
On 7 Mar 2008, at 20:25, Winter, G (Graeme) wrote:
Hi Pietro,
I would use pointless for this - it will correctly reindex the
reflections and sort them to
In ccp4i Scala task, click to open the Excluded data panel, click on
Exclude selected batches
There you can define one or more ranges of batches or lists to exclude
If you just want to exclude the last part you can define a range eg
301 to 999
You don't need to explicitly define runs
On Fri, Mar 14, 2008 at 5:11 PM, Phil Evans [EMAIL PROTECTED]
wrote:
In ccp4i Scala task, click to open the Excluded data panel, click on
Exclude selected batches
There you can define one or more ranges of batches or lists to exclude
If you just want to exclude the last part
I've had some problems getting recent versions of Pointless to link in a
portable way, due to a new call into the CCP4 library, this can cause
segfaults on some systems. I keep hoping someone will tel me how to get
round this (a ccp4 routine calls getpwid which apparently cannot be
static)
You
This problem probably dates from when I updated my machine to Leopard
It shouldn't be too difficult to build from source: the Makefile shuld
(more or less) work
It will be in the imminent(ish) new CCP4 release 6.1
Phil
Thanks Graeme - the ppc version works fine on my intel machine, both
It's odd because coot gives flat riboses even if you remove all the
torsion info from the dictionary
Phil
On 1 Jul 2008, at 15:31, Jim Naismith wrote:
I don't know how many of you are frustrated with AO5* in NADP NAP
(and in
NAD). I trolled the web looking for a solution but did not find
Scala has an option (ANOMALOUS MATCH INRUN) to select matching
Bijvoet pairs, which will have a similar effect to average DelAnom,
but when I've tried it, it has given worse results than just chucking
everything in together
Phil
On 23 Jul 2008, at 16:53, Bart Hazes wrote:
Jacob Keller
Perhaps obvious - are you sure the space group is C222 not C2221?
Phil
On 25 Jul 2008, at 14:19, Roger Rowlett wrote:
Carl Soja wrote:
Dear all
I tried to solve one structure by ccp4i molrep(resolution at 3.0 A,
space group C222, sequence ID 30%). I can get a good Rfactor 0.528
at first
If I've go a superposition transformation (x' = Rx + t), as it happens
from a superposition in ccp4mg, how do I get the position direction
of the rotation axis (to draw in a picture)?
I know that any (orthonormal) transformation can be represented as a
rotation about an axis + a screw
, but at present I think it gets it wrong with multiple
datasets.
I'll look into it
Phil
On 29 Jul 2008, at 23:07, hari jayaram wrote:
Hello Phil Evans,
Thanks a lot for your reply. Pointless worked great to edit XNAME
and DNAME for unmerged mtz files.
We are now taking multiple crystal
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