Hi Ganesh,
two things I'd advise that might make a difference for you:
1. Improved media for better expression
See Protein production by auto-induction in high-density shaking
cultures by W.F. Studier Protein Expression and Purification 41 (2005)
207-234
(there's also a
Hi Yang.
Adding to what Phoebe has said below, remember that when running polyacrylamide
shift gels using TBE and in the absence of SDS, your protein (depending on its
charge) may not migrate into the gel, or may in fact migrate out of the well
altogether (in the absence of DNA binding).
In
On 13/09/10 14:30, Oganesyan, Vaheh wrote:
I have coordinates of “small” molecule in pdf format, i.e. its an
image of pdb file and it doesn’t let me select text. The molecule has
150 atoms, so doing it by hand is not an option. How would one go
around it?
The molecule is polymyxin B and
Dear Vaheh,
the PDF-file is not a proper PDF-file. It is an image encapsulated into
PDF, which is why it does not contain any text!
You could try a text recognition software. In the Linux-/Unix-world, gocr is
probably to most popular one. Since it is a courier font, your chances should be
pretty
What you could try to do is print out the pdf file, then locate a
scanner with a suitable scanning software. Several scanning software
have the possibility of generating word processing program output or
ASCII format. Since the pdf file is text only (no figures etc) then it
should be OK. You
can get 3D mol file from chemspider, too. And convert to pdb with one of many
display progs. But whether it is exactly the same as what is in the pdf file is
an exercise for the user ;-)
J
From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of
Does anyone know of a program that will mutate a given base in the pdb of a DNA
structure?
Many thanks in advance.
Rex Palmer
Birkbeck College, London
Hello fellow crystallographers,
I am trying molecular replacement for a protein crystal dataset that has very
high sequence similarity to the search model with several predicted flexible
loop regions; however, all attempts at finding a solution have not produce very
ideal starting solutions
For OCR without installing software, Free OCR http://www.free-ocr.com/ works
quite well for me, but beware that you may need to do corrections
afterwards.
Just upload your file to this web site, as long as it isn't secret!
The OCR in Adobe Acrobat works better for me though, and is worth the
Does your model structure form a dimer? Maybe best to search with that
model..
eleanor
Paul Holland wrote:
Hello fellow crystallographers,
I am trying molecular replacement for a protein crystal dataset that has very
high sequence similarity to the search model with several predicted
On Mon, 2010-09-13 at 15:52 +0100, Paul Holland wrote:
that has very high sequence similarity to the search model
How high exactly?
--
I'd jump in myself, if I weren't so good at whistling.
Julian, King of Lemurs
Dear CCP4 members,
I have finally used Eleanor's idea, and it works very well. After
applying SSM, we can get a rotation matrix(M), and a displacement vector N:
(Xnew,Ynew,Znew)'=M*(X,Y,Z)'+N
Then, from the rotation matrix M, we can get its another representative
format-*quaternion
Hi Rex,
If you have to mutate only few bases, maybe you can proceed manualy with
coot. And maybe after mutate refine at less for geometricals parameters
of your new base.
Nicolas.
Le 13/09/10 16:43, Rex Palmer a écrit :
Does anyone know of a program that will mutate a given base in the pdb
Here is how I would approach this:
Use Phaser to search with monomers, or
dimers if you suspect that the biological unit is composed of dimers
and have reasonable guess at a dimer search model.
Also consider searching with N- and
C-terminal truncated search models. Sometimes a
Hi Yuan
You might want to look at the 'exponential map' as an alternative to
quaternions. This article evaluates all the various representations
of rotations, including Eulerian angles, polar angles, rotation
matrices, quaternions etc:
Try balbes from G. Murshudov's website. It will find proper search model
and use proper truncations automatically. In addition, it will put in
your sequence.
Paul Holland wrote:
Hello fellow crystallographers,
I am trying molecular replacement for a protein crystal dataset that has very
Thanks go to all who took their time and answered and in some cases did
file manipulations. Extremely helpful! Not only for this particular case
but many times CCP4BB has proven to be the best.
Below are received answers in chronological order:
Albert Gluskov: I converted it in adobe acrobat pro,
Thanks, lan.
For quaternions, it needs w^2+x^2+y^2+z^2=1, thus reduces variables to 3.
But fortunately,(x,y,z) here only represents a direction of the rotation
angle, and the absolute value of them are not that important.
I think a rotation vector and the rotation angle could be a very good
==
Beamtime available at CHESS, October 13 - December 7, 2010
==
The CHESS/MacCHESS facility, located at Cornell University in Ithaca, NY,
invites macromolecular
Hi Ganesh,
I agree with all comments below. You might want to check if it is
indeed impurity or degradation.
If it's impurity, in my case, improving expression level dramatically
increase purity. 8-His worked better than 6-His. You said you get
optimum results at 20mM NaCl but got more
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