Dear Garib,
Thank you very much. I will try the keyword.
> Your case: Do you see some sort of modulation of intensities in your images?
> Something like weak strong intensities along c axis? Or do you see elongated
> peaks in the images.
Sorry I'm not sure what "modulation of intensities in imag
Hi Gloria,
My hobby is space group symmetry.
My interest phenix development.
> so I can't imagine a protein crystallographer
> would ever need to apply the modulation function to a protein atom
> that happened to be on one.
That's true. Protein residues don't have internal symmetry, therefore
Dear Yamashita
Refmac indeed does not apply vdw repulsions (antibumping restraints) if the sum
of occupancies is less than 1 and atoms do not belong to the same residue with
the same alt code. It means that if you have two or more molecules each with
occupancy less than 0.5 then there will be n
Dear all,
Following Pierre and Harry's suggestion, problem solved using xdsme -i
'ROTATION_AXIS= -1.0 0.0 0.0'" image_name_*.img. Thank you very much.
Good luck for everyone
Cheers,
Donghui
On Thu, Dec 9, 2010 at 12:39 AM, LEGRAND Pierre <
pierre.legr...@synchrotron-soleil.fr> wrote:
> Hi ag
Dear Bosch,
Ye, at the moment, I don't know if the geometry of my beamline 13B1 at
Taiwan take the same direction as in the script. How can I get this
information? Directly ask beamline scientists at Taiwan? or if there is some
log files which may contain such information during data collection.
08 December 2010
Dear All,
Below is a summary of answers I obtained for my questions on “Blotting paper
for plasmid DNA”.
Thank you all very much for your quick response and thanks to CCP4BB.
-Partha
__
Hideaki Moriyama:
How about FTA filter papers (Whatman).
https://dgrc.cgb.indi
Dear Garib,
Sorry I'm a little confused.
As Eleanor said, Is it true that Refmac doesn't apply vdw restraints
if the sum of the atoms occupancies is <= 1?
> If you want to deal with translational disorder (e.g. you have a modulated
> crystal then there is another way.
In my data, there are crys
I've gotten some interesting responses, that I will summarize for the
group later, but I thought I should clarify why I asked.
I was worrying about this because I have been working out the steps in
how to determine the (3+1)D superspace group for a protein crystal.
The last step listed in IT vol C
Dear all,
just to add that Clemens Vonrhein already a few years ago has implemented a
procedure
similar to the one Simon describes, to automatically fill the cavities in the
macromolecule
before computing the mask for the solvent, thus avoiding placing solvent where
the core of the protein is,
My fellow crystallographers,
I wanted to take a poll.
How many of you have ever had a protein atom on a Wyckoff position
(AKA a special position).
What kind of molecules have you found at special positions (it would
have to contain the symmetry of the special position, right?)
I'm thinking it is i
OK, I see. I looked at my log-files, and I also have about 30
restraints for for VDW_symm. Then I looked at another structure with no
packing issues, and the corresponding numbers is ~90. What I am saying
is that the number of restraints that you have appears to be reasonable.
It seems that cla
Dear All,
Apologies for non-CCP4 / non-Crystallography question.
I planning to spot plasmid DNA on a blotting paper for transport. I do not
have any idea what type of blotting paper is used for this purpose.
1. what type of blotting/filter paper should be used? will any type of
Whatman paper is
In refmac you can remove vdw interactions between chains using the following
command
It is an example:
vdwr exclude between chains A B
or between resdues:
vdwr exclude between residues first residue 123 chain A second residue 155
chain B
Regards
Garib
On 8 Dec 2010, at 16:09, Keitaro Yama
At the moment there is no way of telling refmac to ignore clashes between
symmetry related atoms.
Is there any reason you would want to do that? Perhaps there are other ways of
solving the problem you would like to solve.
I can add a keyword to force to ignore these clashes if there is sufficien
As far as I know there are no repulsions restraints applied if the sum
of the atoms occupancies is <=1.0. If one atom is fully occupied. and
another partial then there will be a restraint.
Eleanor
On 12/08/2010 04:45 PM, Keitaro Yamashita wrote:
Dear Ed,
These tables were reported by Refmac5
Keitaro,
The Python script we used to make Fig. 1 is contained within the
Labelit source code distributed with Phenix, in the file
labelit/publications/sublattice/sublattice_Fig1.py
The PDF-generating code was never made into a finished product; at
present the most important missing element is t
Dear Ed,
These tables were reported by Refmac5:
Before refinement,
---
Restraint type N restraints Rms Delta Av(Sigma)
.
VDW repulsions: symmetry: refined_atoms 38 0.232
On Thu, 2010-12-09 at 01:09 +0900, Keitaro Yamashita wrote:
> When I tried to refine using Refmac5, the output told many vdw
> repulsions with symmetry mates
What do you mean by that? I had a similar situation recently, and there
are many records in the log file that say something like this
IN
Hi Keitaro
perhaps we should discuss this discreetly off-board!
Yes, you can make a picture on the command-line with prediction boxes. I do it
frequently.
If I take one of our example HypF images (see
http://www.ccp4.ac.uk/autostruct/testdata/mosflm/hg_images.tar), then on the
command line I
Dear all,
I'm refining complex structure against X-ray diffraction data with
packing disorder.
(Some domains overlap with their symmetry mates (4-fold), so their
occupancies are set to 0.25)
I'd like to know whether refinement programs can exclude any
interaction among symmetry mates from geometr
Thanks Tim, our mails must have crossed :-)
@ Donghui:
This is the standard JOB card
JOB= ALL !XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT
what you probably need is after running the first time xds in the directory to
go back into your script and change it into
JOB=DEFPIX XPLAN INTE
Dear Harry,
Do you mean that it cannot be done in command line to make picture
with prediction boxes?
I wrote input file for ipmosflm, by which I had only to click
"Predict" to see the predictions on GUI.
(I wrote matrix, symmetry and mosaic spread information in the input file!)
Or, how can I g
Dear Donghui,
only because XDS shows a warning about an inaccurate solution does not
necessarily mean that it did not index your data correctly.
Check the file IDXREF.LP (from bottom to top - log-file are usually more
interesting that way round). There should be a summary of the refined values a
Marian,
It seems that XDS does matter detector type Q315 or Q315r. Same crystals
when collected at ESRF Beamline 23-1 using Q315 detector can be processed
straightly with the provided script from XDS website and I only need to
input ORGX=1536.0 ORGY=1536.0 for indexing or data integration. If XDS
I don't see the job card in your script.
So it will assume job= all and then it is more than normal that xds will
complain about the indexing being inaccurate. Look at the idxref.lp file and
pick your space group then rerun xds adding job=devpix
See what happens
Am on my phone will send you my sc
Dear All,
A final reminder about next month's CCP4 Study Weekend entitled "Model
Building and Refinement and Validation". The meeting will run from the
5th to the 7th of January and will be held at the University of Warwick
in the UK. We have a limited number of places left and the deadline for
re
Hi
I think the phi rotation on that beamline is the opposite way round to most
other Q315s - so in Mosflm you'd need to have a "DETECTOR REVERSEPHI" line (or
click the "reverse direction of spindle rotation" box in iMosflm). I don't know
what you'd do in XDS, but I don't think there is anything
Hi Keitaro
You should get the predictions on the images using Mosflm if you supply a
matrix & spacegroup. Running the "create_image" part after indexing in iMosflm
means that the matrix, symmetry and mosaic spread are all available, so it can
be easier doing it this way.
There's a very old scr
Dear Boaz and Harry,
Thank you very much for your suggestions.
As pointed out by Harry, I think it is difficult to automatically make
a picture of spots labeled with their indexes..
But I have never known that iMosflm could accept the commands of ipmosflm.
I'm glad to hear that and it worked ver
Dear all,
Thank you very much for your valuable inputs. This is an update based from
the suggestions.
Following Pierre's suggestion, I installed xdsme (
http://code.google.com/p/xdsme/) and run it. xdsme extracts image header as
the below:
Image format: adsc
Detector type: ADSC 315
D
Postdoctoral Research Fellow
Structural Biology of DNA Repair Complexes - Ref: 120
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
School of Life Sciences
UNIVERSITY OF SUSSEX
A Cancer Research UK-funded Postdoctoral position is available immediately in
the laboratory
The DVD COMPATIBILITY: Zone 0, compatible with players anywhere in the world.
The DVD is available from Hampton Research
http://hamptonresearch.com/product_detail.aspx?cid=26&sid=196&pid=606
and
Triana http://www.trianatech.com/
Kind Regards, Bob Cudney
__
In Europe:
http://www.trianatech.com/
Mark van Raaij
On 3 Dec 2010, at 19:25, Bernhard Rupp (Hofkristallrat a.D.) wrote:
> FYI, crystal fans. Really worth watching, and with X-mas approaching perfect
> gifts for the crystals in your life. BR
>
> From: JuanMa GarciaRuiz [mailto:juanma.garciar..
is this DVD ok or available in Europe, i.e. with the correct regional DVD
digital rights format etc.?
Mark van Raaij
On 3 Dec 2010, at 19:25, Bernhard Rupp (Hofkristallrat a.D.) wrote:
> FYI, crystal fans. Really worth watching, and with X-mas approaching perfect
> gifts for the crystals in y
On 12/07/2010 09:38 PM, Arnon Lavie wrote:
Hi there:
The situation: We are facing difficult molecular replacement: we believe
we have two molecules in the ASU, but phaser/molrep find only one. Using
the electron density calculated using this single molecule, we have
manually placed the 2nd molec
Hi Keitaro
Mosflm has been able to output jpegs with predictions for many years - it can
also output ppm files (which are not compressed in a lossy way, so probably
better for zooming in or converting to other formats). However, you'd need to
add the indices to the prediction boxes manually -
Hi,
There are a number of possibilities that come to mind:
1. Use the "ROTATE AROUND" option of the brute-force rotation function in
Phaser to generate a set of rotation angles similar to your real-space
solution, then use each of these for a full translation search.
2. Use my old program BE
If the two molecules are related by translational symmetry, at least
Phaser is not happy.
Since in the second rotation function it removes contribution from the
first orientation,
if the orientation/rotations of the two molecules in identical, it
will fail to see the
second rotation applies.
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