,
but the GUI does not populate the corresponding fields. Normally I
thought an orange highlighted field is a mandatory field that needs
some data…
Windows ccp4 6.3.0-020 updated
Best, BR
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
Of A Leslie
Sent: Thursday, May 16
Hi Bernhard,
When I have used the "convert" program via ccp4i, the cell and
symmetry have indeed been read from the mmcif file and written to the
MTZ file.
Andrew
On 16 May 2013, at 13:50, Bernhard Rupp wrote:
Dear Developers,
I wonder if there is any particular reason why, if present
Dear Sebastiano,
This is not entirely straight-forward.
The Oxford English dictionary gives the first definition of "freeze"
relevant to this discussion as:
"Of (a body of) water: be converted into or become covered with ice
through loss of heat"
This is cer
Dear Theresa
In response to your first question, one way to do this is to look
closely at the image (eg changing the contrast level) with the
predicted pattern superimposed after indexing, or alternatively just
integrate the image and look at the reported mean I/sigmaI as a
function of re
Hi Andreas,
The simple answer to this is that you do NOT
attempt to redefine the background. Providing the additional spots
shown in your image belong to the same lattice, mosflm will
automatically exclude pixels from adjacent spots when doing the
background plane fi
Dear Bhupesh,
The first thing is to check that you are
using the latest version of mosflm (7.0.9, 14th May 2012). If you are
using this version, then please send me more details of the problem
and ideally some images.
Best wishes,
Andrew
On 17 Sep 2012, at 09:
It is possible to force Pointless to select a particular solution,
using the "Find or match Laue group" option in CCP4i. The default
option here is "Determine Laue group" but if you select the "Choose a
previous solution" checkbox you can specify the solution you want
Pointless to select,
Dear Xinghua,
Other have already commented on the fact that
if the spots are overlapping, even if you adjust some parameters to be
able to integrate the data and get a reasonably complete data set, the
resulting intensities will have some systematic errors that may ca
There is a significant problem that affects the autoindexing in the
latest release of iMosflm (Version 1.0.6, March 2012).
The indexing solutions themselves are not affected, but the suggested
solution (highlighted in blue) will, in some cases, be a solution with
a higher symmetry than th
Hi Vijay,
The obvious person to answer this is Phil Evans, but he
is in New Zealand at the moment and may well not be reading Emails, so
you might need to wait until he is back in the UK (1-2 weeks). I know
that he felt the POSTREF option was not an important one to maintain,
On 15 Feb 2012, at 23:55, Bart Hazes wrote:
Diffracted intensity goes up by the cube of the wavelength, but so
does absorption and I don't know exactly about radiation damage. One
interesting point is that on image plate and CCD detectors the
signal is also proportional to photon energy, s
Dear Madhu,
While I cannot be certain without knowing
what detector was used to collect your diffraction image, ".osc" is
the usual suffix for Rigaku detectors and these will normally be read
automatically by mosflm (just use the "image" keyword with Mosflm, or
use
For some reason it would appear that the message below was not
distributed to ccp4bb when I sent it this morning, JISCMail
recommended that I resend the message, apologies if some have already
received it.
Andrew
Dear Munan,
First of all, you want to consider if th
Dear Bryan,
As Mark van Raaij pointed out you have complete
flexibility in specifying the images to be used in autoindexing or in
cell refinement.
However, the default behaviour is to use the first image and a second
image that is as close as possible to 90 degrees away f
.
I don't understand why these differ (unless Phil change the ADN.cif
entry here for some reason).
I think we need a comment for the library people !
Cheers
Andrew
On 15 Mar 2011, at 14:23, Ian Clifton wrote:
On 15/03/11 12:57, A Leslie wrote:
…
I then try using LIBCHECK standalo
Dear All,
I simply want to create a PDB file for adenosine from the existing
monomer library entry ADN.cif. Normally I do this using COOT (get
monomer) but when I try this I get the following error:
: _lib_update 12/05/10
: --
: ERROR: number of monomers
I have to say that I don't fully agree with James' recommendation to
adjust the GAIN in MOSFLM until the calculated SDFAC parameter in
SCALA is 1.0.
(Background information, the sigmas from Mosflm sd(I) are corrected in
SCALA according to
sd(I) corrected = SdFac * sqrt{sd(I)**2 + SdB
Dear All,
spotted a mistake in my response, please see the correction below (in
bold):
There are a host of caveats in this procedure. For example, if the
images contains significant diffuse scatter around the Bragg spots,
the BGRATIO may be above 1.0 ... this is probably the commonest
e
Dear Bryan,
The quick answer is no. As David Waterman
mentioned, it has a default value for the gain for each type of
detector that it can deal with.
A more detailed answer. An incorrect value for the gain can be
indicated by values of the BGRATIO which differ signific
X-Ray Facility Scientist
MRC Laboratory of Molecular Biology
Cambridge
£26,022 – £31,758
We wish to recruit an Investigator Scientist to join the MRC
Laboratory of Molecular Biology X-ray facility in Cambridge, UK. You
will provide support for a range of projects involving X-ray
crystallogr
Dear Francis,
The quick answer is no. My initial advice
would be to process the data in the usual way, but treating the images
starting at "phistart" as one "run" and the images starting at
"phistart+180" as a different run. This makes a number of assumption
howeve
Dear Fulvio,
Mosflm attempts to read the phi start and end
angles from the image header, but on some synchrotron beamlines this
information is not written correctly to the header, which would
explain the error message. Alternatively, if you have really collected
a "st
Hi Pietro,
There are monomer library entries for Ca in various states of
coordination by water, entries, OC1, OC2,OC3 etc but unfortunately
these are incomplete (no distances or angles with sd's), at least in
our CCP4 installation. The entry for octahedral MG-O6, file MO6, is
complete so
Hi Fred,
If your tetramer show negative cooperativity between the 4
sites for ligand binding, then it is possible to get a tetramer with
(say) only one subunit occupied by ligand, which can introduce
considerable asymmetry if ligand binding gives rise to a hinge type
closure of
Dear Anja,
I'm not sure why you want the orientation of the
molecule in pymol, but working out the orientation of the crystal at
phi=0 is straightforward in imosflm.
Read the image, index it and go to Strategy". In the strategy pane it
gives the angles between the a,b,c a
The biannual Gordon Conference on Diffraction Methods in Structural
Biology will be held at Bates College in Lewiston, Maine from 18-23rd
July. The program covers all aspects of macromolecular structure
solution
from crystallization to structure solution and refinement and includes
sessions on
Dear Simon,
mosflm does indeed estimate the intensity of
overloaded reflections, and these are rejected by default in SCALA,
but you can choose to include them using the appropriate keywords
(ACCEPT OVERLOADS). The number of overloads in the MTZ file, and the
number a
Just a reminder that there is still time to register for the Gordon
Conference on Diffraction Methods in Structural Biology, that will be
held at Bates College in Lewiston, Maine from 18-23rd July.
The program (see below) covers all aspects of macromolecular
crystallography, from crystalliz
The required keystrokes are described (although somewhat hidden) under
the heading "What's new in version 1.0.0" in the imosflm web page. (www.mrc-lmb.cam.ac.uk/harry/imosflm/ver104)
.
There are good reasons for this option not being well advertised. One
is that if keywords entered in thi
The biannual Gordon Conference on Diffraction Methods in Structural
Biology will be held at Bates College in Lewiston, Maine from 18-23rd
July. The program covers all aspects of macromolecular structure
solution from crystallization to structure solution and refinement and
includes sessio
Scientific Programmer
£20,074 - £27,271 per annum
A two year position is available for a programmer to continue the
development of iMosflm, the Graphical User Interface for the MOSFLM
program package to process X-ray diffraction data from crystals of
biological macromolecules. The interf
Dear Clemens,
Yes, this should be possible.
If you click on the Cell or Spacegroup line in the "Images" pane, and
then click on the current value, the field becomes editable and you
can type in your new values.
Best wishes,
Andrew
On 8 Dec 2009, at 17:41, Clemens Grimm wrote:
Dear all,
X-Ray Facility Scientist
MRC Laboratory of Molecular Biology
Cambridge
£26,022 - £31,758 per annum
We wish to recruit an Investigator Scientist to join the MRC
Laboratory of Molecular Biology X-ray facility in Cambridge, UK. You
will provide support for a range of projects involving X-ray
Scientific Programmer
MRC Laboratory of Molecular Biology
Cambridge
£20,074 – £27,271 per annum
A two year position is available for a programmer to continue the
development of a new Graphical User Interface for a widely used
program package to process X-ray diffraction data from crystals of
This discussion seems to have moved a very long way from the original
topic, and hence the reported "Subject", could this be continued as a
new thread please ?
Thanks
Andrew
On 17 Nov 2009, at 11:40, Morten Kjeldgaard wrote:
Tim Gruene wrote:
Yes, but models that can be validated again
BB members may be interested to know that the 2009 Nobel prize for
chemistry has been awarded to Venki Ramakrishnan, Tom Steitz and Ada
Yonath for their structural work on the bacterial ribosome.
I would like to thank Justin for his summary of this topic, which I'm
sure many people found of interest, and is very much in the spirit of
the bulletin board.
I would just like to correct one factual error, in that it has been
possible to specify anisotropic resolution limits to MOSFLM for
37 matches
Mail list logo
