hello everyone
Does anybody knows why refmac5 will not process any model that
contains thymine in its structure? This problem only happens on my PC
which supports a 2.1.0 version of ccp4i. The error in the log file
says its due to bad value during floating point read. However, this
proble
Postdoctoral Positions Available for Experimental and Computational Methods
Developments for XFEL-based Crystallography
Faculty and staff of the SLAC Accelerator National Laboratory and Stanford
University are leading an effort to develop methods for structure determination
of challenging bio
We seek a post-doctoral scientist with strong background in protein
biochemistry and structural biology, and interest in novel drug discovery to
address the unmet medical need in rare diseases.
The Metabolism & Organelle Biogenesis group (MOB) at the Structural Genomics
Consortium, University
Hello All,
I have been working on a structure for one of the research groups here
and have come across a peptide fragment of about 10 residues. The
protein forms a tetramer and the peptide is found between two of the
monomers. The protein itself does not require a peptide for function
Hi Theresa
I'd read Jim Pflugrath's 1999 paper in Acta D - "The finer things in X-
ray diffraction data collection"
Pflugrath, J.W. (1999) Acta Cryst D55, 1718-1725
http://journals.iucr.org/d/issues/1999/10/00/ba0030/ba0030bdy.html
To my mind one of the best and most accessib
Dear crystallographers
What does 2D (Mosflm?) and 3D (XDS?) profile fitting means for data
integration? What is the guideline for using either one?
References to any literature is highly appreciated.
Thank you.
We have an Olympus SZX-12 microscope and are running a 1X objective
(with polarizer) and a 10 X eyepiece. The scope will zoom from
approximately 10X-90X magnification. At 90X a 400 nL drop in a 96-well
plate will nearly fill the field.
Cheers,
___
Roger S.
I was [too] obliquely alluding to this thread...
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27056.html
JPK
On Wed, Jul 18, 2012 at 12:32 PM, Edwin Pozharski wrote:
> http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html
>
>
>
> > Rsym...what's that?
> >
> > JPK
> >
> > On Wed, Jul 18
http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html
>
Rsym...what's that?
>
> JPK
>
> On Wed,
Jul 18, 2012 at 9:12 AM, Edwin Pozharski
>
wrote:
>
>> As has been
shown recently (and discussed on this board), Rsym is not
>>
the
>> best measure of data quality (if any measure at all):
>>
>>
ht
Rsym...what's that?
JPK
On Wed, Jul 18, 2012 at 9:12 AM, Edwin Pozharski wrote:
> As has been shown recently (and discussed on this board), Rsym is not the
> best measure of data quality (if any measure at all):
>
> http://www.sciencemag.org/content/336/6084/1030.abstract
>
>
>
> > narayan viswa
Hello,
I am planning to purchase a stereo microscope for visualizing crystallization
drops. I would be very grateful if someone let me know the “objective” and
“binocular
eyepiece” specifications for SZX-7 or SZ-61 (Olympus) to get good
magnification.
Thank you.
Regards,
Prasenjit
Can you check space group in your mtz and pdb? I have seen this happening when
they disagree.
It is annoying and I would like it to be sorted out. If you want you can send
your data and I can try to sort it out.
Garib
On 18 Jul 2012, at 17:50, Deepthi wrote:
> I tried opening the model with o
How about trying some ARP/WARP?
JPK
On Wed, Jul 18, 2012 at 11:54 AM, Pavel Afonine wrote:
> What happens if you do a round of refinement in phenix.refine after you
> have done the mutations? Note: Phenix Autobuild is a tool to build your
> model, not refine it (though it does some refinement i
Thank You so much . I am trying to process the data again in all space
groups possible for primitive hexagonal and try refinement again. And i
didn't use Phenix after i got the MR solution. Probably refining the
mutated model again would give some more information.
Thank You once again. Appreciate
What happens if you do a round of refinement in phenix.refine after you
have done the mutations? Note: Phenix Autobuild is a tool to build your
model, not refine it (though it does some refinement internally but may not
be as fine tuned as your data/model may require).
Pavel
On Wed, Jul 18, 2012
Dear all,
thanks a lot for all your comments and suggestions for the alignment. I tested
already the pdb server, which works great and I am currently installing a few
other programs mentioned (Chimera, Prosmart.) for comparison.
Best Regards
Christian
Am Freitag 13 Juli 2012 16:30:57 sc
I tried opening the model with other spacegroups MTZ file. The map doesn't
fit well for other spacegroups. The initial model was refined using Phenix
Autobuild software. I tried MR with every spacegroup possible in primitive
hexagonal. Only p3221 worked. There is no twinning in the crystal. I will
Hi there,
Not much information provided. How was the initial model refined ?
Phenix ? It could be a problem with the Refmac refinement protocol
(difficult to say with so little information) if you switched from
Phenix to Refmac.
How certain are you 1 - of the space group; 2 - that the crysta
Refmac takes its spacegroup fro the MTZ file, so if it isn't P32 2 1 then the
refinement will be wrong. You may have to change the spacegroup in the file
Phil
On 18 Jul 2012, at 17:28, Deepthi wrote:
> Hi all
>
> I am working with a small mutant protein which is 56 amino acids long. The
> cry
Dear All (possible candidates!),
there is a call for PhD fellowships in the framework of the multidisciplinary
PhD school in
MOUNTAIN ENVIRONMENTS AND AGRICULTURE
http://www.unibz.it/en/sciencetechnology/progs/phd/phdmountainenvironment/default.html
A 3 year PhD fellowship is available to a s
Hi all
I am working with a small mutant protein which is 56 amino acids long. The
crystal diffracted at 1.4A0 and the space group is p3221. I did molecular
replacement using Phenix software with all the data (1.4A0) and got a
solution. Phenix did auto building with waters and R-free was 0.3123.
Postdoc position in Molecular Neuroscience at Ecole Normale Supérieure
(Paris)
Team: “Glutamate Receptors” ( http://www.biologie.ens.fr/neuronr/ )
Location: Institut de Biologie de l’Ecole Normale Supérieure (IBENS),
Paris, France
Start date: September 2012.
We seek to hire a highly m
I like the Fisher AB15 meter. Large LCD display for presbyopic eyes, and
it will do multipoint calibrations. Most laboratory grade pH meters will
do multipoint calibration, however. We typically do a 3 point pH
calibration at 4, 7, 10, but you can do more if you like. I pair this
with a refilla
As has been shown recently (and discussed on this board), Rsym is not the
best measure of data quality (if any measure at all):
http://www.sciencemag.org/content/336/6084/1030.abstract
> narayan viswam wrote:
>> Hello CCP4ers,
>>
In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI
narayan viswam wrote:
Hello CCP4ers,
In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & Rsym
224.3 %
for multiplicity 7.8 and completeness 98.2 %. I solved the structure by MAD &
refined it
to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is not twinned.
The
Hi Narayan
My only comment would be that P622 is a fairly uncommon space group
(currently 43 PDB entries excl homologs), but obviously that doesn't
mean it's wrong - just worth double-checking! Just out of interest
what's the CC(1/2) statistic for your highest shell?
Personally I specify more bi
Hello CCP4ers,
In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & Rsym
224.3 % for multiplicity 7.8 and completeness 98.2 %. I solved the
structure by MAD & refined it to Rfree 27.3 %. Ths crystal belongs to P622
space group and it is not twinned. The water content is 68%. I low
Two Windows-specific problems have been reported and fixed yesterday:
- cif_mmdic.lib is in %CCP4%\share\ccif, should be in %CCP4%\lib
- rapper doesn't work (missing DLL)
cif_mmdic.lib can be moved manually, so if you don't use rapper there is no
need to update. Installer with fixes is available f
Dear all,
I would like to share with you some problems I am experiencing with a protein,
in case someone has an idea about what it is going on:
I am working with a protein module that gets trapped in Ni-NTA or glutathione
beads. If the protein is purified without tag (ion exchange plus gel
fi
29 matches
Mail list logo
