Hi Folks,
There appears to be a problem with the CCP4 automated downloads pages right at
the moment - downloads are coming down with nothing actually in them! The same
files are available through the ftp site at:
ftp://ftp.ccp4.ac.uk/ccp4/current
Instructions may be found here
http://ccp4
Hi Sabine,
Although the GUI may still work, iMosflm needs a number of other odds and ends
which should be included with tcltk++ - if you asked for these as part of the
download it should work at least from the command line - are you using the same
tcl/tk/blt from 6.0.2? If so the easiest thing
heed Ronan's point about having the ccp4i project
> set up *before* running iMosflm from ccp4i, so that the directories
> are properly assigned.
>
> On 7 Jan 2009, at 08:32, Winter, G (Graeme) wrote:
>
>> Dear Paula,
>>
>> The tcltk++ binary either from
Dear Paula,
The tcltk++ binary either from the downloads pages or
ftp://ftp.ccp4.ac.uk/ccp4/current/extras should work fine - if you unpack this
somewhere, export CCP4I_TCLTK appropriately and add the lib directory to the
LD_LIBRARY_PATH it should solve your problem. If you would like more deta
Dear Francisco,
Is this directory in your load library path? I assume not, given your error,
which suggests you need to source the ccp4-others.setup from setup-scripts file
appropriate for your shell - this sets up the paths etc. for everthing which is
not actually ccp4.
Best wishes,
Graeme
Dear James,
I have just tried this on a linux binary installation and it appeared to work
fine. Please could you tell me what platform you are running on?
Many thanks,
Graeme
CCP4 Support Team
-Original Message-
From: CCP4 bulletin board on behalf of James M. Vergis
Sent: Sun 12/21/2
Dear Victor and BB,
For reasons which are opaque at best some linux distributions name this file
libtermcap.so, and some libtermcap.so.2. Evidently the binary worked fine on
the collection we tested. Fortunately there is a relatively simple if inelegant
fix:
cd $CLIB
ln -s /usr/lib/libtermcap.
Dear Eric,
A native installer for CCP4 6.1.0 for this platform is available from
the download web page:
http://www.ccp4.ac.uk/download/downloadman.php
this is a disk image and installs in the usual manner for macintosh
applications. This includes all of the components needed.
Best wishes,
Dear Victor,
The CCP4mg package is just about to be updated to version 2 built around
Qt rather than the old Python/Tcl/Tk version. The former version was
highly platform specific and would have required rather a large number
of system permutations - this would make the load on the server as you
Dear Engin,
Yep, I can reproduce this using a binary installation myself - that
would be a bug. We (CCP4) will look into it and get a fix to you as soon
as possible.
Thanks for the report,
Graeme
CCP4 Support Team
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac
Hi Andrzej,
To get iMosflm working you need a few extensions which it uses to be
available. A 'full-fat' Tcl/Tk with everything added which will work for
both CCP4i and iMosflm can be found at
ftp://ftp.ccp4.ac.uk/ccp4/current/extras
(Tcl-Tk++-osx-universal.dmg.gz)
This will install by default
ely absent.
Ron
On Thu, 11 Dec 2008, Winter, G (Graeme) wrote:
> One of the many facilities in pointless is to search for absences and provide
> a list of likely spacegroup choices based on the results. It includes
> adjustments for neighbouring spots to address one of Eleanor's conc
One of the many facilities in pointless is to search for absences and provide a
list of likely spacegroup choices based on the results. It includes adjustments
for neighbouring spots to address one of Eleanor's concerns. NCS can cause
reflections to be systematically absent too.
The program can
Hi Frank,
This is an interesting point, and also relates to the knee-jerk
reactions to e.g. Rmerge > 100%. Certainly for the sqrt(1/(n-1)) term
the assumption is that the meaurements come from the same underlying
population so that increasing the number of observations should increase
the accuracy
the checksums.
It is not "York" but the CCP4 core team at Daresbury who will need to do
this, and we will.
Thanks & best wishes,
Graeme
-Original Message-
From: Tim Gruene [mailto:[EMAIL PROTECTED]
Sent: 04 December 2008 10:11
To: Winter, G (Graeme)
Cc: CCP4BB@JISCMAIL
Dear Michael,
How did you do the download? I have just downloaded this file using the old
fashioned command line ftp method, and it worked fine. I expect that there has
been an error somewhere in the transmission.
If you fetch the file from:
ftp ftp.ccp4.ac.uk
cd ccp4/6.1
get ccp4-6.1.0-core-s
Hi Folks,
Appropos to the comments below - if the folk who bundle CCP4 in this way
would be kind enough to send the packages to me, I can test them the
same way as we test our own binary builds, to make sure they work
correctly. Saves me trying to search them out on the web.
Many thanks,
Graeme
Hi Folks,
The idea of comparing different data reduction packages is an
interesting one. It is not however without challenges as alluded to by
Kay. As far as I can see there are two main challenges - the first is
that different users when given the same tools will do different things
- in challeng
Hi Simon,
If you output no merge original index from scalepack, and (I assume)
don't impose any symmetry on the data, so scale in P1, pointless will be
able to work with the output. You will need a relatively recent version
of pointless though, from
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre
Best,
Gra
On behalf of Monica Wesley:
Research Associate (Staff Scientist Structural Biology & X-ray Science)
Cornell High Energy Synchrotron Source
?The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron
Source (MacCHESS) is seeking to fill a staff scientist position. Applicant
Dear BB,
Many thanks for the ~100 responses I received - I appreciate the time
you have all taken to respond. Here are the results so far, which I will
assume represent a statistically valid sample. To be clear though - what
follows is not a recommendation for what systems are good! I have also
no
Dear BB,
I hesitate to ask this, but here goes. If you are a Linux "admin" user (i.e.
the person who installs CCP4) please could you drop me a line (personally,
rather than the BB) about which version of Linux you are using. This will allow
me to figure out the most popular systems people have,
blem I had encountered was coot.
Thanks to everyone who got in touch,
Best,
Graeme
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Paul Emsley
Sent: 20 August 2008 15:34
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot and OS X Leopard
Winter,
Hi Folks,
I have an OS X leopard machine which I would really like to get coot
working on, but it appears to involve messing with the X system and / or
fink, neither of which I really fancy. Now I appreciate that there is
something broken about the X window (no idea what though) but I was
wonderi
Hi Simon,
This looks like you do not have the CCP4 environment set up, which
pointless needs. Have you sourced the appropriate setup script, e.g.
. /usr/local/ccp4-6.0.2/bin/ccp4.setup-sh
Best,
Graeme
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf
Hi,
For MR/SAD/MAD data, the JCSG have made most of their data available -
the processed data at a number of stages (integrated, scaled etc.) and
quite a lot of the raw diffraction data. If you google "jcsg" they are
the first hit. If you look at the structure gallery you can download all
the fil
Hi Dave,
I have been using 1.2.16 on this platform for a long while now and it is
working fine - take a look at the MRC ftp site to see if you can get the
same binary:
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre
Cheers,
Graeme
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTEC
Hi Francisco,
If your real mosaic spread is quite a bit larger than the oscillation width
(which I guess is likely) then you have either fine or very finely sliced data.
I would be tempted to give this a go with a 3D profile fitting program, for
example XDS or d*TREK, which are more optimally
Dear Eike,
Installing XDS is in fact pretty straightforward - if you unpack the XDS
tarball containing the executables "somewhere sensible" - e.g.
/opt/px/xds or /usr/local/xds then put wherever you unpacked this in
your path it will work fine.
You can do this by adding this to your .bashrc file:
Hi Adam,
The symbolic link approach does not work - I hit this problem with
another (C++) program. Your pointer about the compat rpm is helpful
though - this is probably the most robust solution. I ended up compiling
from scratch when I hit a similar problem.
Best,
Graeme
-Original Message
Hi Pietro,
I would use pointless for this - it will correctly reindex the
reflections and sort them to boot. You can specify the correct
pointgroup and reindex operator to reindex the reflections, and (I am
99% sure) pointless will compute the correct unit cell...
You can find recent versions of
Hmm...
Thinking about this it may not be too hard to do with XDS. May involve a
certain amount of fiddling though.
If you do the first stages of XDS processing, namely XYCORR, INIT,
COLSPOT & IDXREF you will end up with a spot file (SPOT.XDS) from
colspot and with indices attached from IDXREF. On
On this note, some tools provide this kind of thing for a fairly small
overhead. Google run picasa on the web which is a no brainer for putting
pictures up on for discussion - this has the advantage that they can
also be "hidden" or "public". Someone has also mentioned blogger as an
option, but thi
Hi All,
A user question about the xia2 behaviour has opened a pot of worms, and
I thought I would ask the community for opinions. If (for example) you
are using an automated data processing or analysis tool, and the
systematic absences suggest a spacegroup choice, what would you like to
do:
(1) n
Hi Lu Yongzhi,
It has to be said it is not obvious. However, there are as far as I can
see at least three possible definitions of I/sigma, so here we go:
(1) I/sigma (calculated, corrected perhaps) for individual observations
- sigma based on counting statistics
(2) Mean(I) / Sigma(mean) - that
The JCSG (www.jcsg.org) have absolutely buckets of high quality
diffraction data which I imagine would be excellent for this task. These
have the advantage of often being MAD data which will give a pretty
decent map with a relatively straightforward shelx / solve script.
Cheers,
Graeme
-Ori
ady scaled intensities and avoid applying the SCALE
>> column again - Phil was the one telling me that. I was scratching my
>> head for a long time trying to understand those various
>> INTIAL/ONLYMERGE/INSCALE/NOSCALE options and how they relate to each
>> other ...
>&
Vonrhein; Winter, G (Graeme); CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Unmerged output from Scala
Hello all,
Along the lines of SCALA options UNMERGED and NOSCALE.. I am a little
confused..
I wanted to get my data from mosflm to be used for the anisotropic
scaling and ellipsoidal truncation
Hi Phil,
I use this option but not these columns. The only time I feed the file back I
use "ONLYMERGE" and "SCALES CONSTANT", to remerge the reflections.
Cheers,
Graeme
From: CCP4 bulletin board on behalf of Phil Evans
Sent: Mon 19/11/2007 5:07 PM
To: CCP4B
Hi Kevin,
I would say that the most useful place for this token will be in
reduced-data land prior to getting phases - so for instance going into
Phaser it could make a sensible choice about what spacegroups to test
based on the accuracy information, likewise experimental phasing / dm
programs. On
I recall that this has been discussed, more than once, on the ccp4-dev
board and quite sensible solutions provided to this, for instance the
inclusion of a one-character flag which would indicate the level of
correctness of the spacegroup information - along the lines of
L => Bravais lattice corre
Hi Justin,
Try exporting GFORTRAN_UNBUFFERED_ALL = 1
Cheers,
Graeme
From: CCP4 bulletin board on behalf of Justin Schmitz
Sent: Mon 29/10/2007 12:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Logfile Problem on Dual-Core Intal Mac with Os X Server 10.4
Hi Bryan,
So, there are two answers to this question. If you are changing the
spacegroup within the same lattice type (e.g. tP) then it is fine (this
is probably what you mean by crystal system) - though you can do this by
just running reindex "symm whatever" afterwards. If you want to change
from
Hi Phil,
Just in case anyone was used to the old default behaviour (and like to use the
current version of Arp/wArp ;oD) could you ensure that there is an option which
will allow the automatic reindexing to the old default setting?
Thanks,
Graeme
From: CC
Hi All,
I heard about a way of preparing crystals - presented at the BSR recently as
"Crystals to go" - which allows them to be carried at room temperature then
cooled for data collection i.e. for beamline testing. Please could someone
point me in the right direction for the instructions on ho
Hi Dave,
I have found in the past that some DVD writers need a bios / firmware
upgrade to be able to cope with the faster DVD's. Usually this is a
windows program you run which overwrites something inside the DVD
hardware itself, which will then work fine for writing. This is unlikely
to be helpfu
ce
cphasematch -mtzin combined.mtz -mtzout dummy.mtz \
-colin-fo "[*/*/F_INFL,*/*/SIGF_INFL]" \
-colin-phifom-1 "[*/*/PHIM,*/*/FOMM]" \
-colin-fc-2 "[*/*/F_CALC,*/*/PHI_CALC]"
Cheers,
Graeme
From: CCP4 bulletin board [mailto:[EMAIL PROTEC
Hi CCP4BB,
Is there a straightforward way to compute the mean phase difference
between two phase columns in an MTZ file, allowing for the difference in
the origin? I am thinking something like:
Cad together two reflection files - renaming the PHIB column, most
likely
Compute phi offset - apply to
Hi James,
The old mar345 images were compressed with the "pack" which Bill is
referring to. This is suppoprted in CBFlib.
PNG and jpeg2000 may well do "better" at compression (would like to see
the numbers with this) but are likely to be much slower than something
customised for use with diffract
Hi James,
On the gathering of the data from all possible beamline / source /
detector combinations below, I am also keen to get hold of these. To
assist with this I have written a couple of bash shell scripts which
will tar, gzip and split into 128MB chunks data, then reverse this
process to ensu
Hi Bill,
> It seems it would be good to have available if we are all going to
> put our images on our web-servers.
Probably easier to either just bzip2 the images (which works reasonably well
but is somewhat slow) or use one of the imgCIF "jiffy" programs to do this,
which will correctly retai
Hi,
I looked at jpeg2000 as a compression for diffraction images for
archiving purposes - it works well but is *SLOW*. It's designed with the
idea in mind of compressing a single image, not the several hundred
typical for our work. There is also no place to put the header.
Bzip2 works pretty much
art transferring gigabytes of
images, all at the same time.
5. I think the NSA might go bonkers over that traffic, although it
certainly has enough storage space. Imagine, they let their decoders go
wild on all those images. They might actually find interesting things in
them...
So, what's the
of
images, all at the same time.
5. I think the NSA might go bonkers over that traffic, although it
certainly has enough storage space. Imagine, they let their decoders go
wild on all those images. They might actually find interesting things in
them...
So, what's the hold-up?
Best - MM
Storing all the images *is* expensive but it can be done - the JCSG do
this and make available a good chunk of their raw diffraction data. The
cost is, however, in preparing this to make the data useful for the
person who downloads it.
If we are going to store and publish the raw experimental meas
... or alternatively just start something on wikipedia?
Just MHO - thought a few times something like this would be useful.
Cheers,
Graeme
From: CCP4 bulletin board on behalf of Kay Diederichs
Sent: Sat 21/07/2007 3:23 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [
Hi Sergei,
I don't think that there is a program available to do what you want, but
I think that the tools are there for you to make one. The biggest
challenge you will have is keeping the mathematics straight!
So, if you start off with something like the DiffractionImage library,
this will help
Hi Rebecca,
The citation I use is from the 2005 CCP4 study weekend:
Scaling and Assessment of Data Quality, Philip Evans, Acta Cryst D 62
72-82.
It is open access from www.iucr.org.
Cheers,
Graeme
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Be
Hi Fred,
Were I you I would take a look at the archive from the JCSG:
http://www.jcsg.org
Most of the structures are around 50% solvent but I would guess that
there are a few which are much higher... I am sure I have come across
one or two... The advantage of this source is that almost all of th
Hi Harry,
The only way I have ever found to do this is to do lots of cad runs.
Especially if you want them all to share the same unit cell, project
name and crystal name...
Cheers,
Graeme
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Harry Powell
Hi,
When you transferred it, did you use FTP from the windows machine? If
so, you need to explicitly transfer it as a binary file otherwise the
ftp program will mess up the file. I expect that this would give the
kind of error you report here. You don't need to do any conversion of
the file.
Chee
eryone who replied - lots of interesting cases to
follow up on and things to check for in future.
Cheers,
Graeme
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Winter, G (Graeme)
Sent: 01 June 2007 11:04
To: CCP4BB@JISCMAIL.AC.UK
Subjec
Hi Folks,
I was wondering if there is a document somewhere explaining some of the
more interesting things which can be interpreted from the plot of second
moment of Z = I'/ anywhere? I've looked around and I can't find much
beyond the things pertaining to twinning, where it will have the magical
v
Hi James,
The easiest way I find is outside the GUI. On a command line type:
freerflag HKLIN foo.mtz HKLOUT bar.mtz
end
Then rename bar.mtz to foo.mtz, and you should find that the job is
done, with 5% of your reflections in the free set.
Cheers,
Graeme
-Original Message-
From: CCP4 b
Hi Lucas,
There is a C++ library called DiffractionImage which may help with #3 if you
get that far:
http://www.ccp4.ac.uk/newsletters/newsletter45/articles/DiffractionImage.html
If you get in touch with Francois Remacle I'm sure he'll send you everything
you need.
Cheers,
Graeme
-Orig
Hi Phil,
Looking at the file it is clear that the end is missing - the files are
identical to a certain point then the last few 0 values are missing and
there is no newline at the end of the ppc version...
I have just run it again on the firewire disk and got the same error,
which is odd. So the
Hi Folks,
Sorry this is slightly off topic. I have an OS X PPC mac mini and I have
noticed some very strange behaviour. When I run scala for one example
the scales file that is produced is exactly 16384 bytes, and when I try
and restore this scala dies. Now running the same scaling job on an
intel
Hi,
I believe that SOLVE can read MTZ format files directly so there is no
need to convert it to anything else. However if you do feel the need to
perform some file conversion I would get mtz2sca (google it) and convert
the MTZ intensities to scalepack format, then read these in as
PREMERGED. That
Dear All,
I would like to announce the latest release of
xia2: Automated Data Reduction
xia2 is a new automated data reduction system designed to work from raw
diffraction data and a little metadata, and produce usefully reduced
data in a form suitable for immediately starting phasing and struct
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