Sangeetha Vedula schrieb:
Hello all,
Apologies for the non-CCP4 question.
I am trying to process some data collected at X6A in March. I edited the
XDS.inp file for ADSC detector. When I try to run xds, however, it gives
an error immediately:
!!! ERROR !!! UNDEFINED DATA_RANGE=
I checked
Department of
Biochemistry and Molecular
Biology,
Faculty of Medicine, Nursing and
Health Sciences
Monash
University, Australia.
http://research.med.monash.edu.au/rossjohn/
The Protein Crystallography
Unit at Monash University, headed by Prof. Jamie Rossjohn, ARC
Federation
Fellow, seeks a
-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 02:45:41 Ian Tickle wrote:
Dear all,
One of my enzymes crystallized in 0.1 M citric acid pH 3.5 and 25% PEK 3350.
The structure solution reveals, citrate molecule is occupying the active
site.
Moreover citrate mediates the dimer formation.
I tried crystallization in the same condition with ligand using soaking with
Hi Leonard
Does the scratch area for the other user exist. Normally this is
$CCP4_SCR/username
Charles Ballard
CCP4
On 9 Jun 2009, at 22:27, Leonard Thomas wrote:
I have ran into this problem before but cannot figure out how I
worked it out. I have setup ccp4-6.1.1 on a redhat
Dear Victor,
Are you using python 3 by any chance? Balbes makes use of the popen2
function for running the underlying CCP4 programs but this is replaced
by the subprocess function in python 3. We'll be updating Balbes to
reflect this change but in the mean time you should try installing an
Dear Victor and Ronan,
BALBES has a new version (1.0.0), with substantial changes in
organization and functionality, implemented on the YORK web server
very recently, you will expect to hear the announcement for that from
Garib very soon. In the new version, the module 'subprocess' or
'popen2'
Hi folks,
I would like to draw your attention to the following job ad:
http://www.embl.de/aboutus/jobs/jobs_embl_ebi_hinxton/2009/w_09_043_ebi/index.html
This is a postion for a senior scientific programmer to work with me at the
Protein Data Bank in Europe at EMBL-EBI in (the real)
A PhD studentship is available to work with Malcolm Walkinshaw
(Edinburgh) and Jeremy Mottram (Glasgow) on the structure-based design
of parasite inhibitors. The funding agency restricts applications to
UK nationals. Please contact m.walkins...@ed.ac.uk
--
Malcolm Walkinshaw
Chair of
Thank you both
Actually, I am using Ubuntu 9.04 Linux and 'python' at the terminal gives me
version 2.6.2. In fact the system has both versions 2.5 and 2.6 (I think 2.5
comes from the previous Ubuntu 8.10, before I upgraded).
Ok. I'll wait for the new BALBES version because on the downloads page
Dear all,
One of my enzymes crystallized in 0.1 M citric acid pH 3.5 and 25% PEK
3350. The structure solution reveals, citrate molecule is occupying the
active site.
Moreover citrate mediates the dimer formation.
I tried crystallization in the same condition with ligand using soaking
with
Hi, All:
Not long ago, I was asking if there was an easy way to convert between
ccp4-formatted maps and cns-formatted maps. Many of you responded and I
appreciate your inputs.
Dr. Herman Schreuder at sanofi-aventis actually wrote a simple script called
HASMAP and he kindly shared it with
The scratch directory was there but it was owned by root for some
reason. After deleting it and rerunning the set up scripts all works
fine.
Cheers,
Leonard Thomas Ph.D.
Macromolecular Crystallography Laboratory Manager
University of Oklahoma
Department of Chemistry and Biochemistry
620
On Thursday 11 June 2009, Ian Tickle wrote:
-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
Then it's clear what the problem is: whichever program created your file
put the wrong space group number in (or copied it from an input file).
For I2 it must be '4005' not '5', no question. This is the number found
in the $CLIBD/syminfo.lib entry under 'symbol ccp4':
begin_spacegroup
number 5
Hi Sangeetha,
Here is an XDS.INP that I recently used to process data from X6A; you
could try inputing your parameters in this file (or at least compare the
two).
Hope that helps, and good luck!
-Chris
--
Christopher Bahl
Dartmouth Biochemistry
7200 Vail Bldg.
Hanover, NH 03755
Phone: (603)
Thank you.
Unfortunately, it doesn't work even now.
On Thu, Jun 11, 2009 at 11:47 AM, Jürgen Bosch jubo...@jhsph.edu wrote:
Hi,you should remove the following lines:
SPOT_RANGE=7 18 !First and last data image number for finding spots
SPOT_RANGE=20 20 !First and last data image
Hi,
you should remove the following lines:
SPOT_RANGE=7 18 !First and last data image number for finding
spots
SPOT_RANGE=20 20 !First and last data image number for finding
spots
and instead define the spot range only in one line e.g. SPOT_RANGE=1 50
That should fix your
Not sure if this is relevant, but all clipper programs (and I think all
programs wince 6.0) take the symmetry operators as the source for the
spacegroup rather than the spacegroup symbol.
So I would expect changing the spacegroup number or symbol would not
affect most programs in any way.
I am just now editing it again using nedit. I edited it before in textedit.
That was probably my problem! And no, when I look at it using more, it is
all messed up.
I edited Chris's file. New error.
!!! ERROR !!! CANNOT READ XPARM.XDS
So now, I followed Jurgen's advice of JOB=ALL and it is
Using the symmetry operators as the definitive source of space group
information, rather than the name or number of the space group, is the
only completely safe approach, and I am pleased to see that CCP4 now
does this. SHELX has worked this way since 1970, though in a moment of
weakness I
mtz2various seems to get the symm info correctly from the header using
LRSYMI but then it calls MSYMLB3 using the SG number '5' (and the
correct name 'I121') which will cause the SG name and the symm ops to be
overwritten with the wrong ones (i.e. those for 'C2'). Again the
problem here is that
Dear Samy,
You mentioned that your enzyme crystallizes in 0.1M citric acid pH3.5 plus
25% PEG 3,350.
I wonder if you have tried to systematically scan for other carboxylic acids
as buffer/co-precipitating salts. I would suggest you to try the serie of
carboxylic acids, citrate, acetate, formate
In fact it's not quite true to say that the symm ops are used as the
definitive source of space group information in all circumstances: where
the SG info is read from some types of file (e.g. MTZ header), but by no
means all (e.g. PDB files don't contain symm ops), then it appears that
at least in
I moved the program to /Applications as well.
When I start XDSviewer giving it the whole path, it errors out, saying:
/Applications/XDS-Viewer.app/Contents/MacOS/XDS-Viewer: line 6: 818 Bus
error
$CURRENT_DIR/xds-viewer-bin
If I double-click on XDS-Viewer.app icon, it begins to
Hi Sangeetha,
1) when I open the XDS.INP that you posted with a text-mode program like
vi , it looks very messy - like one long line, with ctrl-M control
characters at the putative linebreaks. I just realize that Tim Grüne
found that out in the same way!
2) Christopher Buhl's JOB= line does
Hi Sangeetha,
On Thu, Jun 11, 2009 at 01:26:14PM -0400, Sangeetha Vedula wrote:
On Thu, Jun 11, 2009 at 1:23 PM, Sangeetha Vedula wrote:
When I start XDSviewer giving it the whole path, it errors out, saying:
/Applications/XDS-Viewer.app/Contents/MacOS/XDS-Viewer: line 6: 818 Bus
error
Sangeetha Vedula schrieb:
Thank you so much for your detailed reply. It did run now, but not being
able to see if it found the spots right makes me nervous. I'll try to
get xdsviewer to work.
Posting the helper program in the wiki will be very useful. I for one
would definitely look forward
I did some tests of s/r MSYMLB3 and the problem seems to lie there, or
at least its behaviour is inconsistent with the documentation, so it may
be a generic problem rather than specifically a problem with
mtz2various.
I just read in the space-group number and name, call MSYMLB3 and print
what
I should say more clearly what I meant. The SHELX programs all use
the symmetry operators INTERNALLY as their definitive source for ALL
symmetry-derived information, whether in real space or reciprocal
space (e.g. in deciding which reflections are systematically absent).
Of course the user very
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