Garib Murshudov schrieb:
What is the version of refmac you arre using. There was a bug and I
think we have fixed it. If you take the version from
www.ysbl.york.ac.uk/refmac/latest_refmac.html it may give consistent
results. Only mac and linux versions are available. For windows
version you
Cytochrome c
Best
CSt
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von
Artem Evdokimov
Gesendet: Wednesday, October 21, 2009 2:25 AM
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Colored proteins :)
Hello CCP4 folks!
I have a quick
Have a look at the phycobiliproteins.
Best,
Tim
From the Pattersn peak it seems very likely that you have two
molecules in the asymmetric unit seperated by the very vector that
seperates your two MR solutions, and both MR solutions are correct?
Or is that not possible? Is there no room for 2 molecules in the
asymmetric unit, and the
People keep asking me if buccaneer can build loops. In response to which
I usually point them to 'loopy' and 'rapper', both of which do an
excellent job.
However, I seem to have written a loop building program by accident, and
since people have been asking I guess I may as well release it.
- E. coli cytochrome b562: the entire culture turns red upon overexpression.
- The bilin-binding protein of Pieris brassicae is a blue protein,
although its chromophore biliverdin IXgamma only occurs in insects.
- The neutrophil gelatinase-associated lipocalin (NGAL) is wine-red
if produced in
Dear crystallographers,
After solving a structure by molecular replacement I have 16 copies of
my protein in the asymetric unit. However in the PDB file they are
scattered over several unit cells.
I would like to know if there is an easy way or software to move all of
the 16 copies close to
You can do it easily in coot:
display your objects.
Then display the symmetry (draw, cell symmetry) with a large enough
radius.
Then File: save symmetry coordinates, click on one atom of one of the
equivalent copies you're interested in.
You have to repeat the process several times. It
Hi All,
Thanks for all the replies, I would like to add more information, after
reindex it to P21212, the cell parameter is a=88.71, b=116.26, c=55.12, the
molecule is a long rod like head to head dimer with a length of 110Å (55Å
long for each monomer) and we used the dimer to search the
Hi everybody,
I solved my first crystalstructure and now want to publish it. But how do I
know the structure is ready for publication and deposition in the pdb. We can
explain our theory with the structure but which factors I have to regard to
publish nothing wrong or bad. Can anybody tell how
A post-doctoral position to study cystoskeletal macromolecular
assemblies using cryo-electron microscopy is available in the Sosa lab.
For this position the ideal candidate will be interested in solving
problems related to the structure and function of proteins and will be
willing to learn or
Dear Katja,
I find the Molprobity server very useful. It analyses key factors of
your structure like Ramachandran plot, rotamer outliers or clashes
and tells you where improvements are necessary. It also ranks your
model in respect to other structures in the pdb of similar resolution
Some redox proteins from sulfate reducing bacteria are expressed at
high levels:
Yellow-brownish APS reductase (FAD FeS)
Brown Hydrogenase Ferredoxin rubredoxin ... (FeS)
Green Sulfite reductase (Siroheme, FeS)
Red c-type cytochromes (1 heme, 4 heme, 9 heme or even 16 heme)
lots of colours!
Hi everyone,
Is there a free utility that can convert an x-ray diffraction image
collected with an ADSC detector to a standard image file format e.g.
.jpg, png, etc.? I'm looking for something more elegant than a
screen-capture that will yield a higher (graphics) resolution image.
I'm sure
Hi Andy,
If you have a recent CCP4 installation (i.e. 6.something I think)
there's diff2jpeg, which does exactly what you want. Otherwise there
are also spells to use Mosflm for this which allows a little more
control over the greyscale settings.
Cheers,
Graeme
2009/10/21 Andy Torelli
Hello FX,
As already mentioned there a number of programs that can perform this task.
If you end up deciding to go with Coot, I put together a play by play that
should help.
http://bit.ly/oHqDW
Hope that helps.
Sean
Hi
Mosflm has done this for years - there's a recipe on the Mosflm FAQ
pages (well, the questions were asked frequently when I originally
wrote them about 7 or 8 year ago!). Someone called Graeme Winter (now
at Diamond) wrote this code originally...)
On 21 Oct 2009, at 15:53, Andy
Hi all,
I will highly appreciate your help regarding following:
How to align two DNA structures in Pymol or Coot or any other softwares?
( I tried regular align in Pymol, but it doesn't work for DNA; it
works great for protein structures.)
Thanks a lot in advance !
Mike
Hi Mike,
By 'align', if you mean superimposition, lsqman will do the job.
Raji
---
Raji Edayathumangalam
Joint Research Fellow
Brigham and Women's Hospital/
Harvard Medical School
Brandeis University
On Oct 21, 2009, at 11:06 AM, Mike England wrote:
Hi all,
I will highly
If using Coot, you can also merge molecules on the original and all symmetry
related pdb files that you saved, which will automatically renumber the chains
for you.
Kendall Nettles
Try MarView: http://www.marresearch.com/download.html#Utilities
I use the Linux_glibc-2.3.3 (RedHat9, WS3, etc).
Just download it, unpack (gunzip marView.gz)
# chmod a+x marView
a) to run the program from terminal
# ./marView or
# kate .bashrc:
alias
A JPEG has fixed colors for the pixel values. A diffraction image has to
use a viewer to convert the pixel values (counts) to a color.
One problem with just using a converter to jpeg is how to convert
intensities to color (i.e. computer display values).
A demo version of d*TREK is freely
Andy,
Why not try labelit.png filename output.png [-large]?
Labelit is availale at http://cci.lbl.gov/labelit
Nick Sauter
On 10/21/2009 7:53 AM, Andy Torelli wrote:
Hi everyone,
Is there a free utility that can convert an x-ray diffraction
image collected with an ADSC detector to a
Both pymol/align and coot/ssm (I presume) do the secondary structure
alignment first followed by structural alignment. So it only works for
proteins. In Pymol, there is fit command that instead matches atoms
with the same names; and super which does sequence alignment first.
You can try to play
Hi Katja,
a possible option:
from main PHENIX GUI select Comprehensive validation. For example, it
will do:
- all Molprobity checks;
- draw POLYGON picture (Acta Cryst. D65, 297-300 (2009) Crystallographic
model quality at a glance.);
- show all kinds of stereochenistry rmsds;
- real-space
Anna Pyle's group came out with a powerful idea- a simplified set of
torsion angles for nucleic acids (NA).
http://nar.oxfordjournals.org/content/vol31/issue16/images/small/gkg682f1.gif
http://nar.oxfordjournals.org/cgi/content/abstract/31/16/4755
This is implemented in a Perl program, called
On Wed, Oct 21, 2009 at 6:20 AM, Katja Schleider katjaschlei...@yahoo.dewrote:
I solved my first crystalstructure and now want to publish it. But how do I
know the structure is ready for publication and deposition in the pdb. We
can explain our theory with the structure but which factors I
ThyX (also known as Flavin Dependent Thymidyalte Synthase, FDTS) is yellow
due to bound FAD.
-Partha
On Tue, Oct 20, 2009 at 5:25 PM, Artem Evdokimov ar...@xtals.org wrote:
Hello CCP4 folks!
I have a quick question - could you suggest a few naturally intensely
colored proteins? Colors based
Believe it or not, you can do this with ImageMagick, which is already
part of most linux distros:
convert -depth 16 -type Grayscale -colorspace GRAY -endian LSB -size
3072x3072+512 \
GRAY:test_0_001.img test_0_001.jpg
where this example turns a binned Q315 image (3072x3072 pixels) with a
Dear crystallographers,
I try to solve a MR problem in P21 with several different structures (and
one EM map) as search models.
I would like all solutions to have the same origin so I could compare them
and see their relative positions.
I think a possible solution is to bring the center of mass
There is a program in the CCP4 Suite called reforigin, which might be
what you want. Since all origins are equivalent, there is no way
a-priori to force an MR program to always use the same origin, all you
can do is compare to a reference. However, a trick you can play on
such programs (that
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Sorry if this is a bit off topic. But I have found it useful. Members of the
ccp4bb might be interested in the biomedexperts network ( www.biomedexperts.com
). Once you join (as professionals of biomed science who have already
published) you have a homepage that gives you recent publications of
Hello Fred,
Thanks for sharing! I have also been looking for ways to keep up on
literature. This weekend, I combined 17 structural journals into a single
RSS feed using yahoo pipes. I did a short post about it here:
http://tinyurl.com/yhp2xlm
I would be curious if others have any tips or
hello
i have 3.25 A data of multidomain protein with 4 individual domain
.one domains structure is already known . and for others domain 40 %
simmilar structure is known . when i am running phaser with one known
domain i am getting the solution but after getting solution i
Dear ccp4bb crowd,
Thank you for the wealth of useful replies to my request! I've received over
100 messages with suggestions!
A crude summary of replies is presented below (I've added PDB ID to most of
these). Overwhelmingly, the preferences tended towards iron-loaded proteins
(red or brown)
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