Hi everybody,
One PhD position is available in the group of Assoc. prof. Thomas
Hamelryck, Copenhagen, Denmark. The subject is inference of protein
structure using state of the art probabilistic methods. Knowledge of
Bayesian probabilistic modelling, machine learning and C++ is a strong
plus.
Dear Crystallographers,
In a former lab we had a script which would read DALI output, automatically
download the structurally-similar proteins, superimpose them, and color by
regions superimposed. That was in the days of O. Does anyone have a
similar-functioning script for CCP4MG, pymol, or
Thank you all for your interest in my books - the response was overwhelming!
All books have found a new home and were sent to their destination with the
addressee informed by mail. Sorry if it wasn't you - I have tried to help
people who are starting up or who are teaching and do not have
Hi Tobias,
We use LabTrove:
http://www.labtrove.org/
Pros:
Relatively easy local install
Revision control
Ability to attach any file
Cons:
clumsy blog formatting
does not lay eggs.
Regards,
Dmitry
It is a bit clumsy being based on a blog engine and does not lay eggs… But it
works
Hi Everyone,
In my 2.5-angstrom structure, there is negative Fo-Fc density
surrounding a metal ion after refining in Phenix. From anomalous
diffraction I am certain of the metal's identity and position in each
monomer. Also, the ion is appropriately coordinated by nearby side
chains. Should I be
I would also be very interested in acquiring such a script, if one exists and
the savvy author is willing to share it.
Jaime
__
Jaime L. Jensen
GRA
Department of Chemistry and Biochemistry
North Dakota State University
email: jaime.jen...@ndsu.edu
Hi Chris,
In my 2.5-angstrom structure, there is negative Fo-Fc density
surrounding a metal ion after refining in Phenix. From anomalous
diffraction I am certain of the metal's identity and position in each
monomer. Also, the ion is appropriately coordinated by nearby side
chains. Should I
I need help with a problem whose dimensions I perceive, but cannot surmount.
It appears to be very important for me to re-make an illustration I made long
ago using molscript. For various reasons, I cannot think of a way to do this
with Pymol. I want to highlight active site residues by
Dear Charlie,
I still use molscript quite a bit, it is not so old fashioned as you
might think. Raster3D is even in the standard repository of Debian.
You need to use the command line option '-r' in order to create Raster3D
output. You can use the pipe
molscript -r -in your_molscipt.inp |
Hi,
I love using the ESCET algorithm developed by Thomas R. Schneider, it
calculates error-scaled difference distance matrices, identifies domains very
precisely, generates pml of aligned and coloured molecules... I just love it.
More info:
http://www.ncbi.nlm.nih.gov/pubmed/10818348
Refining the occupancy will help your R-factor and flatten your density,
but you need to be careful to also refine the B-factor of the metal
ion. Don't refine both the occupancy and the B-factor during the same
run (the two are correlated at this resolution), refine the occupancy of
just the
I have used CNS before, but not for this sort of refinement. I see in
the bindividual.inp file that I can select atoms to be included--it
is defaulted at known and not hydrogen. Do you know the proper
nomenclature for selecting a Zn ion in chains A and B?
Thanks,
Chris
On 5/6/14, Steven Herron
Straightforward in Refmac...(a CCP4 package)...
From my iPhone
On 6 May 2014, at 18:02, Chris Fage cdf...@gmail.com wrote:
Hi Everyone,
In my 2.5-angstrom structure, there is negative Fo-Fc density
surrounding a metal ion after refining in Phenix. From anomalous
diffraction I am certain
13 matches
Mail list logo
