From a practical point of view, a solution for documenting grouped
occupancy refinement should at minimum allow
(a) easy automatic harvesting from the respective refinement log
files, and
(b) equally easy extraction from the PDB/cif format to replicate the same
refinement
(c)not
Hello to every one
Can any body send me the information in concise form about
history of protein crystallization along with what is the properties of
protein crystal in lattice parameters.
Thanks In advance
Sanjit Kumar
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Hi James,
I would say that 0.333 (in a scientific context) implies that I am
confident about this number up to the third decimal point, i.e. 0.3325
= x = 0.3334. This gives you an idea of the precision. 1/3 is not a
scientific format, but a
Hello to every one
Can any body send me the information in concise form about
history of protein crystallization along with some idea about the
properties of protein crystal in lattice parameters.
Thanks In advance
Sanjit Kumar
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Dear yamei,
my guess is that the download was not completed, or your hard disk is
about to break. Try downloading it again. You can also copy files from
the command line with the cp command.
Best,
Tim
On 07/24/2014 07:19 AM, Yamei Yu wrote:
Hi
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[flame] It's all there in the shelx format. If someone would write a
wrapper to translate it into mmCIF, everybody would be happy with the
least necessary effort [/flame] ;-)
Cheers,
Tim
On 07/24/2014 10:46 AM, Bernhard Rupp wrote:
From a practical
Dear all,
the early bird registration deadline (July 30th) is approaching
fast! Register the soonest to have a discounted fare.
Students and young researchers: there are some slots available for oral
presentations and some funds left for travel grants. Submit your abstracts
Hi Sanjit,
These two reviews throw some light on the history of protein
crystallization:
http://www.ncbi.nlm.nih.gov/pubmed/24165393
http://www.ncbi.nlm.nih.gov/pubmed/25005076
I didn't understand what you exactly mean by properties of protein crystal
in lattice parameters .
DEAR ALL
I am trying to solve the structure of a protein DNA complex with molecular
replacement. The resolution in about 2.5 angstrom. The spacegroup is P21.
The search model has about 50% identity and is a dimer of a dimer. The
problem is the unit cell is huge and so the number of molecules in
Try using DNA as a search model - this has worked very successfully in our
hands before.
Tony.
- - - - - - - - - - - - - - - - - -
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton,
Hi Tim,
I download it again through command line and got another error message:” -bash:
/Users/yamei/xutil_osx/osx_moleman2: Bad CPU type in executable
It seems the software does match my CPU. The processor of my computer is: 2.3
GHz Intel Core i7
Do you know how to solve this ?
Thank you so
In addition to that good suggestion, with a model at such high sequence
identity and with reasonable resolution data, it would be a good idea to search
for smaller models, like a single dimer or even a monomer, because the assembly
may have changed conformation. Another possibility you should
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Dear Yamei,
I am not sure where the official site for USF is now, but I would use
http://xray.bmc.uu.se/usf/
There you can download OSX_binaries for Lion and Snow Leopard. The
file in the tar-archive is called 'usf_osx_bin/moleman2' rather than
Not sure why this qualifies as a flame or who you want to flame - seems
reasonable
but needs to be done so that the data items are extracted consistently from
all programs
and can be interpreted again by the refinement (or validation) programs
independently
of which program they came from. Insular
Hi Mark
Unless you've done something very odd, Snow Leopard binaries should be
compatible with Mavericks (and Yosemite, too, when you get to try that).
Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge Biomedical
How do I use DNA as search model? Can I use it in molrep or phaser?
On Thursday, July 24, 2014, FOOS Nicolas nicolas.f...@synchrotron-soleil.fr
wrote:
Dear Yang,
you should try different search model, for example :
1) DNA only,
1) DNA
2) protein
1)DNA+Prot
etc... You can also try to
You can use molrep or phaser as you prefer with DNA.
To do that, you can edit you pdb file by hand with your favorit text editor
(vim, emacs...)
And you can cure your pdb file with Edit PDB File in ccp4 coordinate Utilities
De : dusky dew
Dear all,
I have a Rigaku MicroMax 007 HF X-ray generator that is cooled by
chilled water supplied rather unreliably through the building
infrastructure. I was wondering what alternatives exist.
Could other MicroMax 007 users share their experiences with alternative
cooling solutions with
Dear Andreas,
we had a similar issue with our MicroMax 007, with a primary water/water
chiller (ATC K3) in between the generator and a secondary inhouse water
circuit.
After a year of reliable service the K3 would shut off occasionally and dump
the 007 with a cooling error. We found that
Dear Andreas,
We have a Hyfra water cooled system (VWK50) on our MicroMax 007,
but it is probably over-dimensioned
because it is also used by a Xstream equipment, a smaller dedicated
cooler to the micromax could be better.
Daniel
Le 24/07/2014 17:53, Andreas Förster a écrit :
Dear all,
I would warn you that the K3 and K9 chillers have internal hoses which cannot
tollerate water pressure above 125 psi. We had a hose fail from the building
chilled loop pressure. So, be careful adding any pressure with a pump before
the chiller...and maybe consider one after the chiller to
Thermo scientific has air/water chillers. Google:
thermo scientific neslab merlin recirculating chillers
brings up the links.
We have one of these cooling an Oxford xcalibur.
It supplies circulating cold water under pressure which
we hook up where the house chilled water would go on
the
Hi Andreas -
My 007HF is cooled by a Haskris R050 chiller which I got from Rigaku.
This has a refrigeration loop inside it to extract heat from the closed
water loop that goes to the generator; the extracted heat can then go to
building chilled water, or even an open loop (city cold water,
Hmm. Maybe I'm doing something very wrong, because I get the following when
I try those binaries:
dyld: Library not loaded: /usr/local/gfortran/lib/libgfortran.3.dylib
Referenced from: /Users/brooks/Downloads/usf_osx_bin/./moleman2
Reason: no suitable image found. Did find:
Hi
Ours is cooled by a Haskris R250, which is sized for an XStream also. While
our heat exchangers have had a couple of issues, overall the Haskris heat
exchangers have performed quite well. They redesigned ours when they found
out about our building chilled water. I'm not affiliated with and
Hello all,
I’d like point you all to the LCP Tool and Technologies Workshop that the
Scripps Research Institute is hosting in Bedford, MA on October 17th. The
workshop is being run by Dr. Vadim Cherezov, and is part of a two day
protein crystallography event in Bedford, MA. Please see here for
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