Hi all,
I would like to ask some questions regarding this thread..
1) What is exactly meant by "Fourier transformed electron density"?-
according to my knowldege performing a fourier transform on the electron
density gives you the structure factor back. So, how does it related to
what Prof. James
Fenghui,
What is your resolution? If your having trouble distinguishing between pro and
leu I am guessing it is
worse than 2.8 A.
You may not be able to model side chains confidently with lower resolution
data. You may have to make a call
on wether or not to model side chains, and if your model
Does anyone have the dictionary file for BrU, as in the brominated
ribonucleotide?
The distributed files include the deoxy version,
5-bromo-2'-deoxyuridine-5'-monophosphate.
Best wishes, Pete
You might want to look at some images of side chain electron density.
http://www.ruppweb.org/garland/gallery/Ch2/index_2.htm
BR
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dialing
Pretty
Sent: Friday, January 13, 2012 2:22 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject:
It's not the strength of the electron density it's the shape that is
important.
Dale Tronrud
On 01/13/12 14:21, Dialing Pretty wrote:
>
> Dear All,
>
> For the electronic density of LEU and Pro in the electronic density map,
> which is much stronger?
>
> For the electronic density of LEU an
Dear All,
For the electronic density of LEU and Pro in the electronic density map, which
is much stronger?
For the electronic density of LEU and Lys in the electronic density map, which
is much stronger?
The reason I ask the above questions is I need to distinguish them in the
electronic de
On Fri, 2012-01-13 at 10:40 -0800, Ethan Merritt wrote:
> Which of these two statements would be more useful:
> 1) The RMSD for sidechain atoms between apo and holo was 0.678 Å.
> or
> 2) Only two residues exhibited a significant change of
> conformation:
Perhaps the same is true for the back
> Let me put it this way. Suppose you were reading a paper about someone
> else's structures. Which of these two statements would be more useful:
> 1) The RMSD for sidechain atoms between apo and holo was 0.678 Å.
> or
> 2) Only two residues exhibited a significant change of conformation:
>th
I think you have to be a little more clear as to what you mean
by an "electron density map". If you mean our usual maps that we
calculate all the time the Patterson map is just the usual Patterson
map. It also repeats to infinity, with the infinitely long Patterson
vectors (infinitely high fre
I am trying to think, then, what would the Patterson map of a
Fourier-transformed electron density map look like? Would you get the
shape/outline of the object, then a sharp drop-off, presumably? Is
this used to orient molecules in single-particle FEL diffraction
experiments?
JPK
On Fri, Jan 13,
On Friday, January 13, 2012 09:07:07 am Appu kumar wrote:
> Firstly thanks to Robert Nicholls for making me aware of the software
> necessary for side chain RMSD calculation. I have installed and now going
> through manual to use it for exploiting the structural differences. Thanks
> a lot.
>
> Se
On 01/13/12 09:53, Jacob Keller wrote:
> No, I meant the non-lattice-convoluted pattern--the pattern arising
> from the Fourier-transformed electron density map--which would
> necessarily become more complicated with larger molecular size, as
> there is more information to encode. I think this will
No, I meant the non-lattice-convoluted pattern--the pattern arising
from the Fourier-transformed electron density map--which would
necessarily become more complicated with larger molecular size, as
there is more information to encode. I think this will manifest in
what James H called a smaller "gra
to echo Tim's question:
If by pattern you mean the position of the spots on the film, I dont think they
would change based on the complexity of the macromolecule being studied. As far
I know it, the position of the spots are dictated by the reciprocal lattice
points
(therefore the real crystal l
Crystallographer
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Firstly thanks to Robert Nicholls for making me aware of the software
necessary for side chain RMSD calculation. I have installed and now going
through manual to use it for exploiting the structural differences. Thanks
a lot.
Secondly, for Ethan Merritt, I am seeking the information for comparing
On Friday, 13 January 2012, Appu kumar wrote:
> Dear ccp4 users,
>Would you please guide me how to calculate
> the RMSD of side chains alone without considering C-alpha backbone.
> Is/are there any program/programs availble which do this job. I want
> to know the RMSD of
Dear CCP4bb readers,
a postdoctoral position and a scientific officer / higher scientific officer
position are available at The Institute of Cancer Research (ICR, Chelsea,
London, UK), to undertakes crystallographic, single particle electron
microscopy analysis and biochemical analysis of larg
Have run into a similar problem.
Cleared the background color by running 2M NaOH together with 0.2M EDTA.
Better replace BMT with TCEP (1 mM).
Also keep in mind that adsorption is pH dependent, that is the higher
the pH, the better is adsorption.
Many proteins adsorb irreversibly above pH 7.0.
That is interesting. It works for me here and for few other people in other
places. Can you exit and restart JLigand, can you send me a figure of what is
happening?
regards
Garib
On 13 Jan 2012, at 11:00, Wolfgang Skala wrote:
> ccp4 is 6.2.0,
> refmac5 is 5.7.0010 (the file you provided; fo
Hi Katherine,
I recommend Zn-IDA Sepharose (Chelating Sepharose Fast Flow, GE Healthcare),
which we have been using successfully for more than 20 years, since the early
days of IMAC:
Skerra et al. (1991) The functional expression of antibody Fv fragments in
Escherichia coli: improved vectors a
ccp4 is 6.2.0,
refmac5 is 5.7.0010 (the file you provided; formerly 5.6.0117),
libcheck is 5.2 (formerly 5.1.14),
dictionary is 5.28
I also tried each of the four refmac5-libcheck combinations, but without
success.
yours
Wolfgang
Ok, I'm completed baffled... and have obviously started something
unintentionally...
NB: it was a joke!
I was amused that Molprobity, after 'adding' hydrogens to my model, had
'improved' the clashscore of my model by an obviously unnecessary number
of decimal places...!
[0.0098 point
That is interesting. Do you use the latest ccp4 and dictionary that comes with
it?
What are the version of dictionary, libcheck, refmac
Just typing
refmac5 -i
libcheck -i
you should get version information. The version of the dictionary is on the top
of a file
head $CLIBD_MON/list/mon_lib_lis
Dear Garib,
thanks for your reply. However, when I use the new versions, 3GP is an
apparently random polyhedron which does not resemble 3'-GMP at all.
Yours
Wolfgang
Dear ccp4 users,
Would you please guide me how to calculate
the RMSD of side chains alone without considering C-alpha backbone.
Is/are there any program/programs availble which do this job. I want
to know the RMSD of side chains for protein comparison.
Thank you in adva
Dear Matt,
We were working with Hal2p a lithium inhibited Ins-mono-PPase like protein 10
years ago.
We had good biochemistry showing that lithium replaced mg at the active site.
We grow crystals in presence of Li and we worked with 1.6 A diffraction data.
Unfortunatelly we did not see any el
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