Next MX-proposal application deadline: March 1, 2010
See:
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Dear All
We perform fermentation using e.coli clone to obtain recombinant protein.
our batch size is 20 L we perform seeeding in two phase i,.e cryovial to
seed 1 then to seed 2 and then in fermentation broth. seed 2 is 10% of
fermentation broth, and seed1 is 10% of seed 2. incubate each for 10 -
Hi everybody,
I have a question concerning a sequence alignment with the sequences of my 4
molecules in the AU. Unfortunately I found out that the sequences of the 4
monomers do not match exactly. I used the program moleman and it showed me the
different numbers of atoms for the monomers. I
Katja Schleider wrote:
Hi everybody,
I have a question concerning a sequence alignment with the sequences
of my 4 molecules in the AU. Unfortunately I found out that the
sequences of the 4 monomers do not match exactly. I used the program
moleman and it showed me the different numbers of
rui wrote:
Hi, Dear All,
I have a mac 10.4 with 4GB memory, I thought it should be pretty fast.
However when I run coot, it's kind of slow. Even when I push the
space key to go to next residue, I can feel it is really walking to
the next residue. Is this normal or something maybe not set up
Hi,
I need someone expert in PYMOL. I am
getting a trouble to prepare a figure to display electron density for some
water molecules. I can see clear density in COOT at sigma level 2.5. But, I
could not see the density in PYMOL even at sigma level 1.0
Here is what I
have done in PYMOL
On Wed, Feb 10, 2010 at 12:16 PM, Raja Dey deyra...@yahoo.co.in wrote:
I need someone expert in PYMOL. I am getting a trouble to prepare a
figure to display electron density for some water molecules. I can see clear
density in COOT at sigma level 2.5. But, I could not see the density in
You have to make sure the asymmetric unit for the maps is the same as for
your molecule (which it probably isn't). The easiest way is to extend the
map so it covers all the atoms with a few angstrom border. Coot
calculates the map on the fly from the mtz file (I am guessing this is the
How are you creating your map for Pymol? You can
find instructions for constructing sensible omit maps using refmac5 and
fft in CCP4 here:
http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Building+and+Validation#Creating_Omit_Maps_for_Ligands_using_Refmac
For displaying omit maps
Hi Raja,
If you are reading in the map saved from coot, it covers just the AU. Most
likely the selection that you are trying to show the mesh around in pymol is
outside of the AU. The solution is to use FFT to draw maps around your model
(it an option in one of the drop down menus in the
The map was created quite long time ago in cns. I have .cv file only. I am
using the same map file both in COOT and PYMOL. I think this a limitation in
PYMOL over COOT.
Raja
From: William G. Scott wgsc...@chemistry.ucsc.edu
To: Raja Dey
Hello,
I've been trying to use harmonic restraints in Refmac by creating a .txt
file with the following in it:
external harmonic residues from 2 H to 4 H
external harmonic residues from 17 H to 19 H
external harmonic residues from 26 H to 28 H
I've used it both with and without the 'sigma'
Hi Jon,
These few rotamers which I fix in Coot, validate in Phenix, refine in
Refmac, and validate again in Phenix keep getting pushed into areas that
are not favored. I would love to hear some ideas as I'm out and this
model
is otherwise done.
did you try refining it in Phenix with or
===
SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT SLS
===
Proposal application deadline: Monday, February 15, 2010
Periods:
May 1, 2010 - August
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