Hi,
I was looking recently for weak anomalous scatterers, when refined model
is known.
I used phaser as described here:
http://www.phenix-online.org/pipermail/phenixbb/2008-July/001136.html
or running phaser from the ccp4 gui SAD with molecular replacement
partial structure
Works very well,
Sloop can generate both a best conformation and ensembles.
http://www.ysbl.york.ac.uk/~cowtan/sloop/sloop.html
Coot has both its own loop building code, and an interface to loopy from
ARP/wARP. If people like sloop we'll add that to Coot too in due course.
Tommi Kajander wrote:
Dear all
I
Hi,
We should probably clarify the documentation on this point. When you
complete the anomalous substructure in Phaser, it's an iterative
process where LLG maps are computed looking for places where anomalous
scattering should be added (or subtracted). New sites are introduced,
and
I hoping for some advice regarding the use of sulfo-NHS diazirine
crosslinker (Pierce) for in vitro protein interaction analysis.
Have tried labeling the protein (8.8kDa, 10 to 20uM conc) with 2 primary
amines using 30-40X of crosslinker in PBS (1hour at 4deg). Have tried other
concentration
Hi Randy,
thanks a lot! That explains everything.
best regards,
guenter
Hi,
We should probably clarify the documentation on this point. When you
complete the anomalous substructure in Phaser, it's an iterative
process where LLG maps are computed looking for places where anomalous
scattering
Dear All,
I have a question regarding the crystallization of lysine and arginine rich
protein around 13%. So far our attempts to crystallize this protein have not
been successful although the secondary structure predictions, CD
spectroscopy measurements clearly show that this protein is folded.
Try reductive methylation of the lysines:
Walter, T. S., Meier, C., Assenberg, R., Au, K. F., Ren, J., Verma,
A., Nettleship, J. E., Owens, R. J., Stuart, D. I. Grimes, J. M.
(2006). Structure, 14, 1617–1622.
Cheers,
Stephen
2009/11/2 Jan Rash jan...@googlemail.com:
Dear All,
I have a
Hi Jan,
We have tried crystallizing a similar protein without success, later on
it turned out that the protein was having a strong interaction with DNA
that was not sequence specific. You might have a case like that
Flip
Jan Rash wrote:
Dear All,
I have a question regarding the
Following on from Stephen's comment. Jena Biosciences sell a kit that
allows you to do it quickly and easily.
check it out here:
http://www.jenabioscience.com/cms/en/1/catalog/529_jbs_methylation_kit.html
We have had success in our lab using lysine methylation to crystallise
an otherwise
Dear Umar,
It's probably not local flexibility or the interaction with other molecules,
such as DNA, that prevents your protein from crystallising but an unfavourable
enthalpy/entropy balance of long side chains which are potentially restricted
by forming crystal contacts. Mutation of
Umar,
Check out: Czepas et al. The impact of Lys--Arg surface mutations on
the crystallization of of the globular domain of RhoGDI, Acta D (2004)
60 275-280. They point out that sulfate ions can help mediate contacts
between arginine residues from neighboring molecules in the crystal.
Before deciding to change the protein sequence it is best to look at the
precipitation pattern of the protein as a function of various precipitants.
If this shows that precipitation is not within the standard range commonly
observed for other basic proteins even at high protein concentrations
Colleagues,
Do any of you have created a def.site file for LRL-CAT 31-ID-D beamline
to be used by HKL2000? I'll appreciate if you can share.
__
Oganesyan Vaheh, Ph.D
Antibody Discovery
MedImmune, Inc.
To the extent this electronic communication or any of its
Dear All,
I need help regarding installing Automar in ferora. After gunzip and untar
the file when I run automar/autiomar-install , it says commant not found.
Can anyone suggest why it is happening and its solution.
Thanks
james
Dear subscribers,
I was having a small problem with a program (compiled with gfortran)
that gave me run time errors when writing to a direct access file.
Fortran runtime error: Record number not allowed for sequential access
data transfer. And I could not figure out why.
So I wrote a
Well, I did hear from the gfortran people... Immediately after I sent my
message to the bb.
So sorry about the post (the error had never occurred on all previous
compilers).
Fred.
---BeginMessage---
On Mon, Nov 02, 2009 at 05:58:09PM +0100, Vellieux Frederic wrote:
Dear gfortran developers,
Check if you have csh installed in your system. If it still fails, try
installing tcsh.
If I am right, then this is happening because automar-install script is
written for csh but which is not installed by default on your system
(most modern linux distros use bash).
On Mon, 2009-11-02 at 22:06
Dear All:
The Division of Human Genetics/Clinical Genetics,
Innsbruck Medical University, seeks to appoint a Group Leader
in Mitochondrial Protein Research for the expansion of a research
focus on the analysis of protein function and interaction in the
pathogenesis of inherited mitochondrial
Dear All,
I used PyMol to generate a qualitative Vacum Electrostatic surface (without
APBS calculations).
Positve and negative potentials are displayed in the range 56.3 to -56.3.
What is the units of these numbers?
Thank you,
-Partha
Oops.., I meant to ask a different quesition. Let me try again:
I used PyMol to generate a qualitative Vacum Electrostatic surface (without
APBS calculations). The potential is displayed in the range -56.3 to +56.3.
Is it possible to change this scale in PyMol, if so how?
Thank you,
-Partha
I just downloaded the new CCP4 package and installed it.
comparing with the old version ( I used CCP4 6.0.2 on my windows xp computer
and finished my Ph.D projects.), I found the new version of coot is kind of
slow in moving to the next residue of the structure by hitting the space. Can
Partha,
Sorry, but PyMOL's built-in potential calculation is qualitative -- if
you care about the actual units, then you should be using APBS instead.
Cheers,
Warren
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
Behalf Of Parthasarathy
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