Hi,
I am using the "MStats" utiliy in UPPSALA-mapman to compare the density
inside and outside of the mask of the model (basically my target is to
somehow quantify the level of noise outside the model mask). According to
the instructions, I need to do:
(1) MAPMAN > re m1 in.map ccp4
>
>
> I've never looked at this statistics before, so I'm a bit surprised
>
So am I !
> - I was expecting a larger discrepancy between Wilson B and average B at
> low resolution. Although this is probably because PHENIX uses Peter Zwart's
> likelihood-based Wilson B estimation (Peter - what's th
Hi Dirk,
this seems to be the case indeed (*):
Resolution_range Wilson_B Average_B Number_of_structures
0.00 - 1.00 9.77 13.11 94
1.00 - 1.25 10.58 16.44 401
1.25 - 1.50 13.50 19.14 1050
1.50 - 1.75 17.20 21.76 3600
1
Dear Hailiang,As James said, the hermitian symmetry of Fourier coefficients,
F(h)=F*(-h), that is known in diffraction theory as the Friedel's law, is an
equivalent of the condition that the corresponding function (electron density)
is a real function.I think if you need further information you
Hi,
I am trying to find best methods for controlled crystal dehydration with an aim
of improving
diffraction resolution (currently at 9A).I have found few references
and success stories about Free mounting system. I would be very grateful if you
can share your
personal experiences with Free mo
Uhh. No. You will only get "imaginary" electron density if your
structure factors violate Friedel's law. I am not aware of map
calculation codes that do this (on purpose).
BTW, "imaginary electrons" are really just "slow" electrons that don't
respond to the x-rays as fast as the "average" e
Dear Sacha:
Yes, I think Fourier synthesis at a finite resolution range will generate
some negative, or more generally imaginary values in real space (hope I am
right again:). For the imaginary values, I think the map should take the
amplitude of it (maybe I am wrong). Do they normally make the de
Hi all
I am trying to run oasis for my SAD data using dual space iteration. I am
using
ccp4-6.1.13 and seems it has the older gui and older oasis version 6.0. I
downloaded the new oasis4 and ran the program with dual space iteraction
option
and end up in normal termination with out any outp
(1) PhD position
One PhD position is available in Dr. Fang Li's lab at the Department of
Pharmacology, University of Minnesota Twin Cities. Research involves
biochemical and structural studies on proteins that guide invasion and
replication of important viral pathogens.
Candidates should be
Cyclized DTT can look similar to this blob. Of course the sulfur
atoms would make one end of the blob more dense than the other.
Dale Tronrud
On 07/09/10 05:12, Nick Quade wrote:
> Dear CCP4 community,
>
> I have solved the structure of a protein in complex with DNA. But,
> inside the protei
Another thing to consider is alternate ligand conformation. The water density
(elongated) and the pocket composition (aromatic) could result in two
alternative binding orientations (of the buffer? I need 3D). I would play
around with models to see if it fits the density.
Paula Lario
#778-828-
Blobology (a branch of macromolecular crystallography).
You could maybe place benzoate in there (the 6 membered ring on "top" in
the pictures), refine, compute a new map and see if you can make
something out of it. Why benzoate: because the ring would find its place
nicely in the "hydrophobic"
Dear CCP4 community,
I have solved the structure of a protein in complex with DNA. But,
inside the protein there seems to be a ligand binding pocket with some
strong density
(*http://picasaweb.google.de/113264696790316881054/Desktop#). *The
protein was in Tris buffer, with some NaCl, MgCl2 an
Prof. Gebhard Schertler
Head of Biology and Chemistry
Biomolecular Research Laboratory
Paul Scherrer Institute
Anfang der weitergeleiteten E-Mail:
Von: Daniel Oprian
Datum: 8. Juli 2010 17:16:43 MESZ
An: gebhard schertler
Betreff: postdocs
Dear Gebhard,
I am writing to find out if you
Hi Tom,
very nice tool! It would be good to get numerical values of the plotted
distributions as well, like mean, median, standard deviation and so on.
Best regards,
Dirk.
Am 08.07.10 15:20, schrieb Tom Oldfield:
Sampath
With regard to your question on what sort of statistics you should g
Stout and Jensen, "X-ray
structure determination", 1989
Solid mid-level theory with practical examples. Most of the hardware
discussed is very dates, but otherwise an excellent intermediate text.
Nic out
Bernhard Rupp wrote:
The question of what textbook to use is very much context sensi
Hi
Sacha is absolutely right here. This was made plain to me during a plenary
session at the recent BCA meeting in Warwick, given by a powder (not protein)
crystallographer - who was using histogram matching density modification, with
negative densities; an expert in density modification in pro
Dear colleagues,
we have the following announcements to make:
8th International NCCR Symposium on New Trends in Structural Biology
2 + 3 September 2010, ETH Zürich, Lecture Hall HG E7, Zürich, Switzerland
For more i
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