Dear Wei,
There is a CCP4 program called Convert to/modify/extend MTZ which you
can use to convert various file types (notably SHELX, CNS/XPLOR, mmCIF,
MULTAN and TNT) to the MTZ format. Look for it in the Reflection Data
Utilities module.
Nothing prescient about that. The MAD concept was first proposed by
Herzberg and Lau in 1967, much before sycnhrotrons were used for protein
crystallography.
Herzenberg, A. Lau, H. S. M. (1967) Acta. Crystallogr. 22, 24-28.
http://scripts.iucr.org/cgi-bin/paper?S0365110X6740
The PNAS
Hi,
Zinc is very much present in the Refmac library.
ZN zinc non-polymer 1 1C
Are you using the correct atom id in your PDB file? It has to be ZN.
Ganesh
Le 14/02/13 21:28, Faisal Tarique a écrit :
Dear all
My protein has Zinc atom but the refmac does not identifies it
Dear Amro,
What you could try is this. Make a solution of 0.5 % (w/v) commassie
brilliant blue in 10% (v/v) ethanol in water. Pipet 1 ul of this into
your drop and close the cover slip. If the crystals are protein, they
should turn blue after some time (typically 30 mins). Salt crystals will
Hi David,
You could try the Glucose Isomerase supplied by Hampton. It crystallizes
under a number of conditions, details of which you can find in their manual.
http://hamptonresearch.com/product_detail.aspx?cid=28sid=56pid=56
Ganesh
Le 04/02/13 17:03, David Roberts a écrit :
So, I know I
Dear Rajesh,
In addition to the R/Rfree, you also need to look at issues like
stereochemistry, bad contacts, clashes, the general fit into density,
unmodelled ligands/waters, Ramachandran outliers, correct side chain
rotamers etc etc. I would advice you to spend (a lot of) time visually
Dear Roger,
In my humble opinion, the qualitative knowledge that the complex
actually forms (established through pull down assays, gel filtration
etc) is probably far more important than the Kd values in solution. In
any case, the crystallization is done at very high concentrations, far
Hi,
Maybe we could just state the obvious, ie, that the crystals were
'Cryo-preserved' in liquid N2.
Cheers
Ganesh
Le 16/11/12 16:27, Enrico Stura a écrit :
As a referee I also dislike the word freezing but only if improperly
used:
The crystals were frozen in LN2 is not acceptable
Dear Careina,
Could you tell what reason you have to believe that your protein is
oligomerising? If your protein is forming oligomers, you should be able
to detect them using crosslinking or Native PAGE.
Do you have access to an analytical ultracentrifuge?
cheers
Ganesh
Le 14/11/12
Dear George,
Le 13/11/12 11:17, George a écrit :
Dear colleagues,
There are some crystallographers with (much) more experience than me.
I ‘ve attached few diffraction images which are not (in my opinion)
typical salt but not typical protein either.
Please let me know you suggestions.
Hi,
First I'm sorry for my blank message earlier.
Doesn't this depend on the oscillation angle? If those images were
collected using 0 to 1° oscillations, I would assume he has a badly
diffracting protein crystal.
Ganesh
Le 13/11/12 11:34, Tim Gruene a écrit :
-BEGIN PGP SIGNED
13, 2012, at 12:40 , Ganesh Natrajan ganesh.natra...@ibs.fr
mailto:ganesh.natra...@ibs.fr wrote:
Hi,
First I'm sorry for my blank message earlier.
Doesn't this depend on the oscillation angle? If those images were
collected using 0 to 1° oscillations, I would assume he has a badly
Hi,
I guess Cacodylate is safe as long as you don't come into direct contact
with it, or dispose it off in a careless fashion. Aren't there
substances in biochemical labs which are a equally if not more harmful,
like acryamide or Ethidium Bromide, for instance?
But I agree that it should be
Douglas,
The elements of a 'vector space' are not 'vectors' in the physical
sense.
The correct Wikipedia page is this one
http://en.wikipedia.org/wiki/Euclidean_vector
Ganesh
On Fri, 15 Oct 2010 11:20:04 -0400, Douglas Theobald
dtheob...@brandeis.edu wrote:
As usual, the Omniscient
The definition of a vector as being something that has 'magnitude' and
'direction' is actually incorrect. If that were to be the case, a
quantity like electric current would be a vector and not a scalar.
Electric current is a scalar.
A vector is something that transforms like the coordinate
circumstances) as vectors.
Checking out of semantics hotel,
Ed.
On Thu, 2010-10-14 at 16:47 +0200, Ganesh Natrajan wrote:
The definition of a vector as being something that has 'magnitude' and
'direction' is actually incorrect. If that were to be the case, a
quantity like electric current
On Fri, 16 Apr 2010 14:31:02 +0530, Hussain Bhukyagps wrote:
Hi!
their is no connection between the metal and ligand in my pdb..
how
can i generate bonds between them using pymol..??
by the way the distance
between ligands and metal is 1.8-2.0 Ao...??
Hussain
Send free SMS to
your
I am sorry for sending that blank email earlier.
Hussain,
A good
way to do that is to use the pymol distance measuring wizard. It draws a
dotted line between the atoms, and writes out the distance in numbers. You
can hide the numbers and leave the dotted line behind.
ganesh
On Fri,
16
Hi Megha,
The two peaks on the HPLC indicate that your protein is
existing in a monomer-dimer equilibrium in solution. The dimerisation is
most probably caused by disulphide bridges. The use of TCEP is breaking
those disulphides and that is causing the equilibrium to move towards the
monomeric
dear Partha,
You could try looking up the biomodels database (
http://www.ebi.ac.uk/biomodels-main/). There must be several mathematical
models in there that may be of use to you.
regards
Ganesh
**
Blow, blow, thou winter wind
Thou art not so unkind
Hi Rui,
In addition to what Fred has advised, you could also try
varying other parameters like temperature and protein concentration. 32 %
is
a very high concentration of precipitant. Maybe you could try using a
bigger PEG (like PEG 8000), at a lower concentration. It worked for me
once.
Hi ,
Maybe the lower frequency of the earthquake vibrations or the
handling helped your crystals nucleate. I would assume that even the
resonance frequency of the linbro plates are low, and may cause
disturbances in them. However, fire alarm systems usually are of a much
higher frequency
Hi Fred,
It could also be that the high impact factor of these journals, and their
'tabloid' character ensures that they are read by more people than other
journals. So any bad data or fraud that gets published in Nature, Cell or
Science is more likely to get noticed and talked about, than
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