Dear all,
I have a question concerning the refinement of partly occupied water
molecules:
in some of my macromolecular crystal structures with resolutions
between 1.1 - 1.4 Å, several round positive Fo-Fc electron density
blobs are detectable which show after assignment of a water
Post-doctoral position at Diamond Light Source, UK
For those of you out there with an interest in methodological/software
development, particularly in experimental phasing, a keenness and ability to
work in a multidisciplinary team at a large scale facility and a desire to work
and live in
You are desribing the reason many people limit their refinement to lower
resolution! I think it is probably universally true that there are multiple
conformations for sidechain/water networks at the surface, which we just
dont model properly. If you are going to tackle the fine details you need
Hard to comment without more information, but check how many molecules you
expect per asymmetric unit. If more than one look at the self rotation
function - it might help.
And you can with difficulty do a cross rotation between two data sets,
which sometimes suggests how crystal 1 is related to
I check ha sites by 1) looking at the shelxe plots ( these are displayed in
the CCP4 GUI task - prob also in phenix? )
If there is good contrast for one hand rather than the other the sites are
likely to be correct - if not - hmmm; there might be a reason but they
could be wrong..
Then I check
Dear CCP4 Users,
CCP4 Core Team is in final stages for 6.4.0 Release. Every release and
subsequent support takes a considerable effort, which scales linearly with the
number of supported platforms. This makes us to periodically revise the scope
of support we can offer to community.
Since at
PS Please consult http://support.apple.com/kb/ht3696 for how to determine your
CPU type. Many thanks -- Eugene
Begin forwarded message:
From: Eugene Krissinel
eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk
Date: 12 July 2013 12:47:26 GMT+01:00
To:
Ditto - I was always impressed with the contraption in the Garman lab which, if
I remember correctly, is made of a thick block of wood and some plumbing pipes.
It is designed to hold empty open Dewars inverted so they could dry.
Edward Snell Ph.D.
Assistant Prof. Department of Structural
Dear Yuan.
1. Is there any programs that could help to compare and check the heavy atom
positions in shelxd solutions? Especially in cases when the solutions are not
obvious. SitCOM seemed very good, is there a 32-bit distribution of this
programs? Or any others have similar functions?
If you
It seems like every couple of years I see an article about a new high
density optical format. Then they don't make it to the marketplace. I
think it has something to do with resistance from the music movie
business over piracy concerns. But anyway, I have learned not to get too
excited until
On Fri, Jul 12, 2013 at 1:08 AM, Stefan Krimmer
krim...@staff.uni-marburg.de wrote:
in some of my macromolecular crystal structures with resolutions between
1.1 - 1.4 Å, several round positive Fo-Fc electron density blobs are
detectable which show after assignment of a water molecule to these
Dear All,
Can anyone please tell me regarding the harmful effects of X-ray , we are
using for protein crystallography, on human being and what are the
precautions we should take.
Thanks
The RCSB Protein Data Bank (http://www.pdb.org) is a publicly accessible information portal for
researchers and students interested in structural biology. At its center is the PDB archive – the
sole international repository for the 3-dimensional structure data of biological macromolecules.
Is this a joke or are you serious??? Hopefully you haven't actually
started shooting people with highly focused X-rays...
Jon
On 07/12/2013 10:14 AM, diptimayee mishra wrote:
Dear All,
Can anyone please tell me regarding the harmful effects of X-ray , we
are using for protein
Most modern textbooks have sections on the proper protections and measures to
take, although the information may be dated. See chapter 6 in Volume III of
the International Tables for X-ray Crystallography. With the modern equipment
and regulatory measures in most countries, you really have to
I dearly love ccp4i, but there is one aspect of the interface that
drives me to distraction. When I type (or paste) an input file name
(let's say input.mtz) into the refmac menu, ccp4i changes various
output file names automatically according to some scheme that doesn't
at all match my work flow.
Hi Krish, You may need to do some construct engineering to get your protein
to express well to the plasma membrane. These steps involve creating many
expression construct variants including N and C-terminal truncations, fusion
partners at the N-or C-termini, or even signal peptides at the
Hi Krish,
Seconding Tim's comments, you may need to switch construct or expression
host. I've seen many times when a membrane protein seems to be in the yeast
membrane, but seems unextractable or most likely, improperly folded. Since
you're already working with yeast, I would recommend trying
We are looking for one or two highly motivated and multi-talented postdoctoral
researcher(s) to join a collaborative project studying the structure and
mechanism of circadian clocks (See Huang et al.
http://www.sciencemag.org/content/337/6091/189.abstract 2012 Science). The
overall goal of
My first reaction to this question was well, it depends. The effect of X-rays
depends on (among other things) the energy (wavelength) and the intensity (and
of course the dose). But I decided not to write about this until...
In response to Michael's note below, I want to point out that
Hi Tim,
Indeed, I engineered several constructs, both N- and C-terminal
truncations, to express this protein in E.coli, yeast and also in BV.
Nothing much success. I'm going to try mammalian cell lines. I have some
constructs with signal peptides and right now I'm trying them. Hope I get
Hi John,
Thank you very much for all the valuable suggestions and the helpful link.
I think it's worth trying S.cerevisiae both for expression and also
protecting the environment from that strong Pichia odour.
Krish
On Fri, Jul 12, 2013 at 3:17 PM, John Lee kw...@msg.ucsf.edu wrote:
Hi
Thanks for the sobering analysis. I would not have expected that.
Fortunately you have to be very persistent to override all the interlocks
on an in-house system. I do know on our Agilent instrument that the
backscatter from a crystal at full power with the doors open is only 3
times
On Jul 12, 2013, at 12:57 PM, Mark van der Woerd mjvdwo...@netscape.net wrote:
I just re-wrote our safety plan because we have to renew our radiation
license for our new in-house instrument. On this plan, they ask you to write
a worst-case scenario. For an in-house sealed tube instrument,
--
***
Anand Srivastava
Scientist
National Institute of Animal Biotechnology (NIAB),
Aryabhata Block,
C.R.Rao Advanced Institute of Mathematics, Statistics and Computer Science
(AIMSCS),
University of
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