Dear Tianlong,
you may use Arcimboldo using e.g. a long helix (or b-hairpin) as starting
model for de novo phasing. If you succeed to phase your structure, you
should be able see if it was part of your protein.
Best wishes
Kornelius
On Wed, Jul 18, 2012 at 6:46 AM, Tianlong Zhang
Dear all,
May I ask for recommendations for pH meters that work reliably over the range
of buffers and components that constitute common crystallization screens ?
Thanks very much in advance.
Anirban
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
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
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
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
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
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 2.5
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
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Team: “Glutamate Receptors” ( http://www.biologie.ens.fr/neuronr/ )
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Paris, France
Start date: September 2012.
We seek to hire a highly
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.
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
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
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.
How about trying some ARP/WARP?
JPK
On Wed, Jul 18, 2012 at 11:54 AM, Pavel Afonine pafon...@gmail.com 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
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
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
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
epozh...@umaryland.eduwrote:
As has been
shown recently (and discussed on this board), Rsym is not
the
best measure of data quality (if any measure at
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 epozh...@umaryland.eduwrote:
http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html
Rsym...what's that?
JPK
On
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.
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.
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
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