Sakamoto-san,
According to XIA2 blog, the new XDS works just fine with XIA2.
http://xia2.blogspot.com/2010/01/happy-new-xds.html
Modify value of supported_versions at line 77 in $XIA2_ROOT/Wrappers/XDS/XDS.py
supported_versions = ['January 30, 2009']
to
supported_versions = ['December 28, 2
Dear all,
I am trying to process some data. When I try to run XDS through XIA2/CCP4i,
it gives an error message was descrived as below.
Status: error "XDS version "December 28, 2009" not supported"
I am using CCP4 6.1.2, XIA2 0.3.1.0 and XDS December 28,2009 with the
CCP4 Interface version 2.0.5
Please note a correction in the time zone. The correct time for the
webinar is 9:00 AM CST so that would be 10:00 AM EST (15:00 UTC/GMT).
Angela
Angela Criswell
Sent by: CCP4 bulletin board
01/20/2010 05:29 PM
Please respond to
Angela Criswell
To
CCP4BB@JISCMAIL.AC.UK
cc
Subject
[ccp4
Raja
You can convert sdf format to pdf via the free ICM-Browser. Download it
here:
http://www.molsoft.com/icm_browser.html
-- read in the sdf file into ICM-Browser and it will be displayed as
chemical spreadsheet
-- choose export to Excel and then save as PDF or use the print to file
option
I would like to draw your attention to an upcoming free webinar series
that will cover several of the most widely used X-ray diffraction data
processing packages. This series is part of a larger webinar program that
focuses on topics 'near and dear' to the crystallographic community.
The first
Dear Friends,
Is there anyone know how to convert sdf file into pdf
file? sdf file contains chemdraw of a number of small molecule compounds plus
some other parameters in different columns. I got a source code for
'sdf2mol.java', but is not working. Any suggestion is apprec
I suppose most have read the Acta D editorial already
http://journals.iucr.org/d/issues/2010/01/00/me0408/me0408.pdf
but it seems another creative way of structure generation
has been discovered by some small molecule people:
http://journals.iucr.org/e/issues/2010/01/00/me0406/me0406.pdf
Best, BR
Hi
I, too, was struck by the potential similarity with Rietveld
refinement, then started to think about the differences. The biggest
difference, of course, is refining against "many" two-dimensional
images compared to refining against a linear plot - so I'd guess in
principle you'd get a
A long time ago I did a bit of Rietveld refinement and I see some
similarities between this approach and what people have been
proposing in this thread. Refining against the profile of the 1-d
powder diffraction pattern rather than extracting integrated
intensities helped to improve the qua
There was a thread a while back which related to this a bit:
"Re: [ccp4bb] Small lines in diffraction pattern (more info)"
In that thread, there were mentioned the papers:
Faure et al NSB 2 Feb 1994
Kajiwara J. Appl. Cryst. (1971). 4, 329
These seem to bear on the issue of diffuse scattering,
Hi Paul,
I'll probably open myself up to criticism (welcomed) but I think I'd disagree
with this somewhat. While crystallography from the Bragg reflections provides a
nice static picture of the structure, looking at the diffuse scatter in more
detail may give more knowledge about mechanism - i.
Jacob-
Based on your question, you would likely be interested in doing some
literature searches for the pioneering work of George Phillips and the
utilization of diffuse scattering information. What you are thinking
about has already been broached - nearly 20 yrs ago. It is likely that
a revisit
Phoebe,
my understanding is that power of UV illumination here is not in
salt-vs-protein test (which, imho, can only be finalized by testing
diffraction) but in improved contrast for protein crystal detection. I
haven't used UV microscopes myself, but images provided by manufacturers
are quite im
Hi Jacob,
I see you're still in the crystallography business.
While you have an interesting idea, I doubt refining structures against entire
images would be of any use in obtaining higher quality macromolecular
structures. Much of what you see on the screen is a function of parameters
complet
Are these things really cost-effective? That is, compared to
the cost of simply posting a list of evil salts like Mg
ammonium phosphate on the wall and testing a few duds in the
x-ray beam?
Phoebe
Original message
>Date: Wed, 20 Jan 2010 13:59:23 -0500
>From: Gabriel Birrane
>Subje
I thought this problem is fixed. Could you please try the version from:
www.ysbl.york.ac.uk/refmac/latest_refmac.html
Problem was that when refmac starts twinning analysis it uses generous
tolerance and then filters out unlikely twin operators.
When large deformation is needed merohedral twinn
Jacob
Yes, discussions have taken place but perhaps more private than on the
CCP4 bulleting board! So I am glad someone has raised the issue.
The present approximation that people make works very well in the
majority of cases. The approximation is implied during the integration
of a spot and is
I received this in the mail today. You may be interested.
http://www.fmpproducts.com
They have products for crystallography
On Wed, 2010-01-20 at 11:28 -0500, Scott Walsh wrote:
> Dear CCP4BB members,
>
> I am shopping around for a UV microscope for the lab and would like to get
> some feedba
I agree with Bernhard -- both on the soundness of the idea and on
the difficulty in finding the right home for it in NSF or NIH, but
I would suggest giving it a try. -- Herbert
=
Herbert J. Bernstein, Professor of Computer Science
Dowling C
Dear Jacob:
I think the main impediment is that more diffuse scattering, for example, isn't
as easy to model as Bragg crystalline diffraction. But it is definitely useful.
One example is tRNA:
http://scripts.iucr.org/cgi-bin/paper?am0009
Acta Cryst. (1994). D50, 210-218[ doi:10.1107/S0907
I think these arguments for image conservation and image *use* are well
taken.
The best source of information of what is going on my be the imgCIF
people, - I'd start with Andy Howard and Herbert Bernstein.
I think that image data (after detector- and configuration-specific
corrections to the raw
Hi Kelly,
since you mentioned you tried refinement in phenix.refine:
I guess I know what the problem is, but I wouldn't tell before I'm sure.
Could you send me the two PDB files: before and after refinement (to my
email, not to the whole bb), and specify which residue/ligand is in
trouble? If
Dear Crystallographers,
One can see from many posts on this listserve that in any given x-ray
diffraction experiment, there are more data than merely the diffraction
spots. Given that we now have vastly increased computational power and data
storage capability, does it make sense to think abou
Hi,
I just found out, that this effect just occurs when I push the "twin
refine" button. I have 4 slightly twinned datasets, and so far the twin
refine worked very well...but this should not happen, I think.
Any explanations or advise?
greetings,
Christian
Hi ccp4bb,
I have a big problem
You are right, NH1 and NH2 are distinct in a way that CD1 and
CD2 in Phenylalanine are not, since the torsion angle that exchanges
them is not freely rotatable (except perhaps in a highly acidic
solution).
The practical difference is that the convention for defining
labels in Phe and the oth
Dear Scott,
We had a UV inspection microscope from KORIMA to look at crystals by UV
fluorescence. It works relatively well but it is expensive ( way too much in
my opinion), you pay for the microscope, the UV source and the software
(named Wasabi) that comes with it
An alternative to that is descr
Joe Cockburn wrote:
Dear BB,
We are trying to solve the structure of a complex between two proteins. We
have two crystal forms of the complex, and a partial MR solution in each.
We now want to average the density between these two forms to improve the
maps, using DMMULTI. However, there are a cou
Hi Tim
If I type findwaters, it finds the command without any problems. Also, Coot
directory is in the same path as in the previous version - that worked fine.
I can't see a clear reason for it not to work from within ccp4i or Refmac...
Any help is appreciated...
Paula
2010/1/20 Tim Gruene
>
Dear CCP4BB members,
I am shopping around for a UV microscope for the lab and would like to get some
feedback
about peoples' experiences using UV microscopes for screening crystals.
Best,
Scott
*
Scott T. R. Walsh, Ph.D.
Assistant Profes
Hi everybody,
sorry for my off-topic question. We would be interested to try bioglass 45S5
in heterogeneous nucleation experiments. Does anybody know a company that
sells it?
Thank you and best regards,
Cédric Bauvois
--
..
Dr. Ce
> Dear CCP4ers,
>
> I want to calculate projections of an electron density map covering a
> molecule along arbitrary directions. Please note: I don't want to
> calculate the usual centric zone projections by using (h0l) zones and
> alike, but really work on the map. Which program can I use for tha
Hi ccp4bb,
I have a big problem concerning refmac_5.5.0088. I refined a couple of
structures. Now after refining I realized that refmac sets wrong
resolution limits for my data. Scaling was done with scala. I cut the
data at 1.8 A. Then I used molrep; respectively difference fourier.
Later in
Dear CCP4ers,
I want to calculate projections of an electron density map covering a
molecule along arbitrary directions. Please note: I don't want to
calculate the usual centric zone projections by using (h0l) zones and
alike, but really work on the map. Which program can I use for that?
Bes
Dear BB,
We are trying to solve the structure of a complex between two proteins. We
have two crystal forms of the complex, and a partial MR solution in each.
We now want to average the density between these two forms to improve the
maps, using DMMULTI. However, there are a couple of things I don't
Dear Kelly,
The way I proceed in these cases is to make a "real" alternative
conformation with the same chain ID and residue number. Example:
HETATM 1260 N1 AEPE L 1 0.875 15.892 20.141 0.50 7.15
N
HETATM 1261 N1 BEPE L 1 0.885 15.884 20.143 0.50 43.64
N
HETATM 1262 C2 AE
Hello all,
I am refining a structure (using REFMAC currently, but have tried with
phenix as well) with a ligand with alternate conformations.
I have added each conformation to the pdb file with 0.5 occupancy and
named as A and B and have been able to refine that.
The problem is only two atoms are
Hi Claudine,
You could also look into the possibility that domain swapping occurred in half
of your proteins. See e.g. Bennett MJ, Schlunegger MP, Eisenberg D. (1995). "3D
domain swapping: a mechanism for oligomer assembly". Protein Sci 4 (12):
2455-68. PMID 8580836
Best regards,
Herman
Hi -
Could the dimer in solution be mediated by an intra-molecular Cys
bridge?
A.
PS I would think that you are maybe a bit too deterministic in your
conclusion ... would it not be better to say that 'the equilibrium
between monomer-dimer does not change in the range of conditions we
t
Hi Paula,
did you check if Coot/bin is in the PATH variable when you start ccp4i?
Maybe the coot executable you run is a wrapper that sets the path which is
not done as you start ccp4i.
Try to type 'findwaters' from the same terminal you start ccp4i from. Does
that yield a 'command not found
Hi all,
We have recently solved a structure that is a crystallographic dimer. We
have performed UCA experiments and we observe a monomer/dimer distribution
in nearly equal proportion. This distribution does not change with protein
concentration, meaning that the two species are not in equilibrium.
Can anybody point me to a protein, or proteins, that can be crystallized but
only as a twinned crystal, even after repeated tries? At this point the
type of twinning is unimportant, but I'm particularly interested in
non-merohedrally twinned protein crystals. Many thanks. GDT
Engineering Associate - Robotics, Sensors and Miniaturization
Membrane Structural and Functional Biology Group
School of Biochemistry and Immunology
Trinity College Dublin, Ireland
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