Hi,
It's not a bad idea to read the Phaser manual for molecular replacement;
see http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement
Soon after the start, in a table on the right hand side, there is: TFZ
score < 5, have I solved it ? No.
Hence with a TFZ score of 3.8 you do not
this is of course possible with PyMOL, try this:
pdbid, chain = '1a00', 'A'
cmd.fetch(pdbid, async=0)
cmd.symexp('__neighbors', pdbid, pdbid + ' and chain ' + chain, 5.0)
print 'Number:', len(cmd.get_object_list('(__neighbors*)'))
cmd.delete('__neighbors*')
cmd.delete(pdbid)
Cheers,
Thomas
On
I was worried as well with the low TFZ score. Usually successful cases with
score >8. I am still puzzled why Phaser and Molrep gave different solutions.
Does this mean molecular replacement do not work out in this case so more
crystals have to be prepared?
A little more information might be helpfu
Have you tried using the DNA as your search model? - I have had success this
way round - certainly more phasing power than your protein model, I guess.
Also, refine with your DNA in place, and your phases/ map should improve -
hopefully allowing you to place your protein molecules with ease.
T
Dear all,
my ccp4 interface 6.1.3 became REALLY slow in response on a new i7 PC with
Fedora core 15
2.6.38.8-35.fc15.x86_64 .
Any ideas where to go from here?
Jan Dohnalek
--
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
A 2-year postdoctoral position is available in the laboratory of Dr. A.
Dessen at the Institut de Biologie Structurale in Grenoble, France, to study
structure and function of new bacterial virulence factors.
The laboratory has state-of-the-art equipment for biochemistry and
crystallography studies
Dear Hubing,
One maybe stupid question: Your are sure the space group is P21 and not
P2 or even something else? Did you test other possible space groups?
Choosing the wrong space group could exactly lead to the results you
observe.
Best,
Herman
From
I also processed with Imosflm and ran Pointless, it was P21. Also it was
indicated by the "Intensity systematic absences" in HKL2000 scale.log file.
Best,
Hubing
On Thu, Jul 21, 2011 at 8:44 PM, wrote:
> **
> Dear Hubing,
>
> One maybe stupid question: Your are sure the space group is P21 and n
Was a SELinux issue.
Jan Dohnalek
On Thu, Jul 21, 2011 at 1:44 PM, Jan Dohnalek wrote:
> Dear all,
> my ccp4 interface 6.1.3 became REALLY slow in response on a new i7 PC with
> Fedora core 15
> 2.6.38.8-35.fc15.x86_64 .
>
> Any ideas where to go from here?
>
>
> Jan Dohnalek
>
>
> --
> Jan Do
We could use HKL2000 for Pilatus 6M detector a few months ago in our lab. We
upgraded our HKL2000 to Version 0.98.701 and asked a new license file to
include Pilatus 6M detector.
Yu
2011/7/20 Petr Leiman
> Dear all,
>
> What is the status of Denzo/HKL2000 availability/support for the Pilatus 6M
Dear all,
I have facing one problem during the refinement of my protein . Actually in my
protein there are some modified amino acids are present like Cystein is
modified into CME which i can get easily from monomer libraray in coot . but
after refinement in Pdb text file indicated some gaps
Hello Afshan,
Maybe the programm that you use for refinement need specific entry with
restraint for your modified amino acids.
More precisely, i think about the *.cif file for exemple.
HTH.
Nicolas
Le 21/07/11 17:13, Afshan Begum a écrit :
Dear all,
I have facing one problem during the ref
Dear All:
We have been trying to crystallize a protein which is large - > 100 kDa.
This is soluble but the best we can get is about 1 mg/mL.
It did crystallize but did not diffract well. Efforts to increase the
concentration has been unsuccessful. I am wondering whether there are
methods that o
You could try loading a small 1ml HiTrap (or similar) Q or S column with your
protein - and knocking it off it in one go with high salt, alternatively
micro-dialysis against a solution containing PEGs can also work well.
Tony
Sent from my iPhone
On 21 Jul 2011, at 17:54, "Narayanan Ramasubbu"
Hi,
Although it's pretty much true that if TFZ>8, the solution is correct, there
are hard cases where a correct solution has a significantly lower TFZ score.
Also, we've been finding that TFZ scores are generally lower for monoclinic
space groups like P21, at least in the search for the first
Dear Members of CCP4BB and PHENIXBB,
Can you suggest a reliable website where I can get basic and advanced
information on protein expression, purification and crystallization. I like
to read on the monitor.
Thanking you in advance...
Hena
Hi Subbu,
You got crystals at 1mg/ml so you probably don't need to concentrate your
protein any higher, especially since you suggest that concentrating beyond that
is problematic. Instead, you may want to try to optimize the crystallization
condition you have already identified. Some possibl
Hi all,
As part of its recent summer update, the Protein Data Bank in Europe (PDBe;
http://pdbe.org) introduced UniPDB (http://pdbe.org/unipdb), a widget for
graphical display of the coverage in the PDB of any UniProt entry (e.g.,
http://pdbe.org/unipdb?uniprot=P19909). The widget can be used
If you are eligible, I'd highly recommend the EMBO courses in Europe or the
CSHL courses in the US on those subjects. Reading is a good start but will
not be enough if you want to do real work.for strategy considerations, there
is always Ch 3 and 4 in le livre.
Best, BR
From: CCP4 bulletin b
See below. I believe Ray intended this to be sent to the entire bb and
especially to Subbu!
And in reading Ray's message, I am reminded that I forgot to mention what he
may be hinting at. You should also try to optimize by creating a fine grid
screen around your identified condition varying i
Dear all,
I am trying to generate a cif file for a new ligand (a sugar derivative)
using "JLigand". The ligand needs to be in D- configuration. However, after
I input the coordinates for this ligand into J ligand and carry out geometry
regularisation, the program automatically converts D configurat
Dear all,
I am trying to generate a cif file for a new ligand (a sugar derivative)
using "JLigand". The ligand needs to be in D- configuration. However, after
I input the coordinates for this ligand into J ligand and carry out geometry
regularisation, the program automatically converts D configura
Dear CCP4BB,
Forgive me for soap boxing, but yesterday the first structure of a
GPCR/Gprotein complex was released (PDB:
http://www.rcsb.org/pdb/explore/explore.do?structureId=3SN6, article:
http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature10361.html).
Recently a student prep
Hi Vineet,
I did not used JLIGAND so far, so I cannot explain what happend, but maybe the
quickest solution would be a manual intervention in the cif-files. Type at at
the chirality remark "positiv or negativ" or whatever nomenclature is used and
save it again. I do it sometimes for my ligands
Hello ccp4 & phenix BB members,
I would like to view the intensity-weighted reciprocal lattice for several data
sets that I have collected. (The data have been indexed, integrated and scaled
with Denzo and Scalepack.) I was wondering if anyone could offer some advice on
what might be the best a
One holistic way to view a reciprocal lattice (or subset thereof) without the
requirement for 3-d or moving frames is with a pole figure.
http://en.wikipedia.org/wiki/Pole_figure
See Palmer & Ladd for a better discussion.
I don't know what software can make a pole figure, though.
James
On
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