You mean something like the animation at the top of this web page?
http://bl831.als.lbl.gov/~jamesh/fastBragg/
This program is a relative of nearBragg, which Dale already mentioned.
-James Holton
MAD Scientist
On Jan 6, 2012, at 5:44 PM, Jacob Keller wrote:
> Actually, as a way to make this
This may give some idea:
Illustration of a molecule and its cosine transform:
http://www.ruppweb.org/garland/gallery/Ch6/pages/Biomolecular_Crystallograph
y_Fig_6-16.htm
and sampled by lattice points
http://www.ruppweb.org/garland/gallery/Ch6/pages/Biomolecular_Crystallograph
y_Fig_6-01_PART3.h
On Friday, January 06, 2012 11:15:11 am Ed Pozharski wrote:
> On Fri, 2012-01-06 at 10:48 -0800, Ethan Merritt wrote:
> >
> > A TLS model is more likely to be appropriate.
>
> A quick clarification request if I may:
>
> We all seen how well the multi-group TLS models seem to match the
> B-factor
On Fri, 2012-01-06 at 10:48 -0800, Ethan Merritt wrote:
> A TLS model is more likely to be
> appropriate.
>
A quick clarification request if I may:
We all seen how well the multi-group TLS models seem to match the
B-factor variation along the chain. Is this in your opinion how such
model may be
On Friday, January 06, 2012 09:30:22 am Nat Echols wrote:
> 2012/1/6 Pete Meyer :
> > However, at 3.2 Angstroms I'd recommend against using atomic B-factors -
> > the "rule of thumb" for this is 2.8 Angstroms for atomic B-factors (or
> > at least it was back in the day). �It might help to use an ov
Francis,
One common response is "try a number of different B-factor refinement
> protocols, use Rfree as a guide to determine which one is appropriate".
I recognize my advice along those lines above -:)
Although now I would say (assuming phenix.refine): "Try individual
ADP refinement first, and
On Fri, 2012-01-06 at 11:18 -0700, Francis E Reyes wrote:
> I've seen the following question asked: At what resolution is
> (individual,group,one per residue, two per residue,overall)
> appropriate?
My personal opinion is that the individual B-factor refinement with
restraints proper to the resol
Pete brings out two concerns: [1] B-factor refinement being stable, [2]
over-fitting at low resolutions. Here I'll suggest low resolution to be in the
3-4A range.
I've seen the following question asked: At what resolution is
(individual,group,one per residue, two per residue,overall) appropr
On Fri, Jan 6, 2012 at 10:00 AM, Pete Meyer wrote:
>
> Thanks for pointing this out to me - I'll have to check out the details of
> how phenix handles it, and give it a try.
>
Details can be found here:
http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf
(page 61 and a
On Fri, Jan 06, 2012 at 09:56:11AM -0800, john peter wrote:
> Hello CCP4BBers:
>
> Could some body send me a sample script to run ARCIMBALDO, the ab
> initio protein structure determination software. Thanks a lot.
That would be a violation of the license agreement (oh noes!).
You can request a
James Holton has software for calculating molecule transform images.
Check out http://bl831.als.lbl.gov/~jamesh/nearBragg/. The program
doesn't read PDB format coordinates, just lists of three numbers.
Dale Tronrud
On 01/06/12 09:44, Jacob Keller wrote:
> Actually, as a way to make this type
This may be true for older software which restraints B-factors only to
bonded atoms, but it is not the case in Phenix*, which takes into
account all nearby atoms, not just bonded ones. The result is that
individual B-factor refinement is very stable at low resolution - we
don't know what the lim
Hello CCP4BBers:
Could some body send me a sample script to run ARCIMBALDO, the ab
initio protein structure determination software. Thanks a lot.
John
Actually, as a way to make this type of figure, I think there are
programs which output simulated diffraction images, so perhaps I could
just input a .pdb file with some really huge (fake) cell parameters
(10,000 Ang?), and then the resulting spots would be really close
together and approximate the
correction:
You should NOT have Rwork>Rfree
First thing I would try to shoot more crystals. Easy way out. I once struggled
with a 2.7A data set for weeks only to find out I had a 1.5A diffracting
crystal taking a bath in some storage buffer right next to my bench.
You mention you have at this point you are looking at 25% rotamer outliers.
2012/1/6 Pete Meyer :
> However, at 3.2 Angstroms I'd recommend against using atomic B-factors -
> the "rule of thumb" for this is 2.8 Angstroms for atomic B-factors (or
> at least it was back in the day). It might help to use an overall
> B-factor combined with one (or a few) TLS groups.
This ma
As others have mentioned, your geometry/x-ray weight may need to be
adjusted.
However, at 3.2 Angstroms I'd recommend against using atomic B-factors -
the "rule of thumb" for this is 2.8 Angstroms for atomic B-factors (or
at least it was back in the day). It might help to use an overall
B-factor
I also had some trouble streaming live.
So I am going to go ahead and also suggest/ask please that the video files be
made available for subscribers and/or all academic users.
Cheers,
Hi all,
I have been trying to solve a protein-DNA complex structure using molecular
replacement. I suspect two copies of protein bind one piece of the DNA, and
the angle between the two copies of protein is somewhere between 130 to 180
degrees. I could get molecular replacement solution using a se
Dear Crystallographers,
has anyone come across a figure showing a normal diffraction image,
and then next to it the equivalent molecular transform, perhaps with
one image as phases and one as amplitudes? Seems like it would be a
very instructional slide to have to explain how crystallography works
> and R-factor/R-free have a value of 0.328/0.326.
Notice that Rfree The question is, as I only have ~3000 reflections, and the atoms in
> the sequence is around 1000, and each atom there are 4 parameters to
> be refined(X,Y,Z,B-factor, assuming occupancy is 1), so how to refine
> my model to avoi
Hello Lisa,
Could the 10-20A be a result of cryo damage as opposed to true packing
disorder? (try collecting a few images at room remp)
If its cryo damage, improve your cryo / try different cryoprotectants.
If its not cryo, just screen about a thousand different crystals from
around the same co
Incidentally the PDB validation server will spit out similar errors if you
have hydrogens on lysine side chains (also not a chiral center) should they
get swapped upon regularization during refinement. It makes the chemist in
me cringe a little bit.
Katherine
On Fri, Jan 6, 2012 at 8:30 AM, Robbi
On Fri, 2012-01-06 at 20:40 +0800, LISA wrote:
> Hi all,
>
> I have a DNA binding protein. I get crystals of this protein by
> co-crystallization with different dsDNAs. But all the crystals have
> very poor resolution, about 10-20A. I tried to purify protein-DNA
> complex before setting trays, but
Hi,
I would like to bethe first in this forum to congratulate the authors of
the two papers describing TAL effector structures! Way to go!
Artem
Due to an as yet unspecified "explosion in a network duct in London", the EBI
in Hinxton (where all PDBe services, including deposition, are hosted) is
currently cut-off from its London data centres (through which all EBI web and
ftp traffic is routed). At present, it looks like normal PDBe serv
Hi all,
I have a DNA binding protein. I get crystals of this protein by
co-crystallization with different dsDNAs. But all the crystals have very
poor resolution, about 10-20A. I tried to purify protein-DNA complex before
setting trays, but it didn't work.The shape of my crystal is not bad.
Please
Hi Afshan,
I assumed, because you mentioned only VAL and LEU, that you were refering to
the CB (VAL) and CG (LEU) as problematic chiral centers. Paul is right that
these atoms are not chiral in a chemical sense, but they are in a computational
sense because every connected atom has a unique n
Charles
I would like to echo what Keitaro suggested - can the archieves of the
talks be made available after ccp4we?
Dave
David C. Briggs PhD
Father, Structural Biologist and Sceptic
University of Manchester E-mail:
david.c.bri...@manchest
Dear Charles,
Internet Explorer and VLC player (thanks, Francis) work for me, but
the streaming stops every few minutes in both ways.
The website should be reloaded each time.
I would be very happy if video archives of talks are available on the web!
Thank you for your consideration,
Keitaro
Hi all,
I have a DNA binding protein. I get crystals of this protein by
co-crystallization with different dsDNAs. But all the crystals have very
poor resolution, about 10-20A. I tried to purify protein-DNA complex before
setting trays, but it didn't work. Please give me some suggestion. Thanks.
l
Hi Yuan,
Bad geometry is a general issue for most low resolution structure
refinement. There are quite a lot papers discussing it. I think you
can try to set a reference structure or set high restrain in
refinement, which should be easily achieved in Phenix. How did you
know the B-factors are too
Hi,
You are touching upon several issues here. The first question to ask is how good and complete are your data to 3.2 A resolution. This should be your first concern. Are they the best you can get at this stage? Second, you're absolutely correct in that there
is a lot more to do to impr
Hi Afshan,
This is not the solution if you are right about the problem being one of
chirality (and it is if it is not and is merely an issue of nomenclature
(as I suspect is the case)). So the question is, if the problem is
indeed one of nomenclature, what software (if any) described it as a
Dear crystallographers,
does anyone know if dialysis buttons for crystallization are available
somewhere in Europe or only at Hampton Research ?
Thanks,
Ulrike
Also, there is one more information I forgot to mention---I also have the
NMR assignment(HNCACB spectrum) of the protein, is it possible to combine
the NMR data in my refinement?
Regards,
On Fri, Jan 6, 2012 at 4:14 PM, 商元 wrote:
> Dear All,
>I have a set of 3.2A data containing only 3000 r
Dear All,
I have a set of 3.2A data containing only 3000 reflections. From the SAD
phasing and iterative modeling and density modification, I get a
preliminary structure with bad geometric conformations(~8/160 ramachandran
outliers in Coot). After Phenix MLHL refinement, the geometry is still ba
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