Hi all
I m just finishing the refinement of several peptide:protein complex structures
and have become unstuck at modifying the N and C terminal ends (of the
synthetic peptides) with the generic acetyl and amide capping groups
respectively. Could some one please explain to me the most straight
FYI for the on-pymol readers.
BR
-Original Message-
From: H. Adam Steinberg [mailto:a...@steinbergs.us]
Sent: Tuesday, June 12, 2012 4:22 AM
To: pymol-us...@lists.sourceforge.net
Subject: [PyMOL] Structural biologist job
Hi all,
A friend of mine is looking to hire a structural biologist
Hi Sonali,
You could try wide-search MR:
https://portal.sbgrid.org/d/apps/wsmr/
Best of luck,
val
On 20 June 2012 19:13, sonali dhindwal wrote:
> Dear All,
>
> I am working on a protein for last so many years and for which i have got
> crystal now in a tray which i kept 1 years ago. It diffra
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello Andre,
what you see is not an error message, it is only a warning message. It
is actually the last message before the remaining output is redirected
to into the ${LOGS} directory.
Paul set up a wrapper "wrap-build-it" for me:
#!/bin/bash
OS=$(u
Hi all,
Is there an easy way to calculate the buried areas between antibody and
antigen for all these complexes in PDB database? Or is there a good
reference have such number? I found an old reference (published in 1990)
reported this number but as more an more structures deposited into the PDB
d
Dear All
I'm trying "build_from_scratch" my coot and it doesn't work... the following
error appears, and I really don't know how to fix it:
Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 7039 (6.9K) [text/plain]
Saving to
I'm not convinced you are not getting lysis but if you want to try
something different use a BeadBeater. They are gentle and very efficient.
Roger Rowlett
On Jun 21, 2012 8:54 AM, "J. Valencia S."
wrote:
> Greetings, everyone. We need to ask your advice on an issue with one of
> our proteins exp
Dear All,
The Laboratório Nacional de Biociências (Campinas-Brazil) and The Membrane
Protein Laboratory (MPL) at Diamond Light Source are organising a Practical
course in Structure and Function of Membrane Proteins.
The goal of the course is to introduce PhD students and post-docs to the basic
Hi all,
In the past couple of years, Mark Harris in Uppsala has developed a bunch of
programs and servers that are useful for crystallographers, structural
biologists and structural bioinformaticians. Some of his programs are listed
here:
http://xray.bmc.uu.se/markh/programs.html
M
can you specify what your cell cracker is.
Thanks,
Jürgen
On Jun 21, 2012, at 9:50 AM, Kelly Daughtry wrote:
If it is inclusion bodies, I generally see a milky solution after lysis.
Have you centrifuged post-lysis and then run an SDS-PAGE?
Kelly
There is something even better than SEC-MALS--solving the structure!
JPK
On Thu, Jun 21, 2012 at 11:16 AM, wrote:
> Dear Raji,
>
> The best way to find out is to run a SEC-MALLS (Size Exclusion
> Chomatography - Multi-Angle Laser Light Scattering) experiment.
>
> Best,
> Isabel
>
>
> -
Dear Raji,
The best way to find out is to run a SEC-MALLS (Size Exclusion Chomatography -
Multi-Angle Laser Light Scattering) experiment.
Best,
Isabel
-
Dr. Isabel De Moraes, MRSC
Membrane Protein Laborato
First of all, isn't the choice either dimer or trimer, and second, as a
protein-detergent complex (PDC), it would be very unlikely that a trimer of
99 kD would run at 100 kD, although all is fair in love, war, and membrane
proteins.
JPK
On Thu, Jun 21, 2012 at 10:50 AM, Raji Edayathumangalam
wrot
CCP-BioSim workshop on QM/MM methods for modelling enzyme-catalysed reactions
School of Chemistry, University of Bristol, UK
Tuesday July 17th 2012
This practical workshop will introduce combined quantum mechanics/molecular
mechanics (QM/MM) methods and their application to modelling enzyme-catal
Hi Everyone,
Sorry for the non-CCP4 post.
I have a very basic question about detergents, critical micelle
concentration and behavior on gel filtration.
A 33kDa membrane protein was purified by gel filtration in a buffer
containing 0.4%(w/v) beta-NG (CMC: 6.5mM) and 0.046%(w/v)LDAO (CMC:
0.14mM).
If it is inclusion bodies, I generally see a milky solution after lysis.
Have you centrifuged post-lysis and then run an SDS-PAGE?
Kelly
***
Kelly Daughtry, Ph.D.
Post-Doctoral Fellow, Raetz Lab
Biochemistry Department
Duke University
Alex H. San
Hi,
I often see no real change in change in solution appearance after sonication
mediated lysis, with proteins which yield low amounts or no soluble protein in
E. coli. I've had a look at the solution post lysis under the microscope and
the cells are infact lysed, it's just the presence of high
Hi,
My favourite first-stop tool: use your cell parameters at
http://www.rcsb.org/pdb/search/advSearch.do
and search for similar Cell Dimensions and Space Group. Or use
ftp://ftp.wwpdb.org/pub/pdb/derived_data/index/crystal.idx
and a short awk script to list similar PDB entries (it's what
Greetings, everyone. We need to ask your advice on an issue with one of
our proteins expressed in E. coli Rosetta cells. This yeast-derived
protein has a very low yield compared to others we work with, and we think
it is because the cells are hard to lyse: even after 3 cycles in a cell
cracker the
Dear Raaij,
We have not done mass-spec on the band from SDS-PAGE
to confirm if it is our desired protein or any other contaminant. So,
cant say for sure.
Regards
--
Sonali Dhindwal
“Live as if you were to die tomorrow. Learn as if you were to live forever.”
--- On Thu, 21/6/12, Mark J van Raa
Dear colleagues,
this is to remind you that the Murnau Conference 2012 on Structural Biology of
Molecular Transport will be taking place from 17-20 October. Online
registration is NOW OPEN on a first come-first served basis
(http://www.murnauconference.de/2012/registration.html).
We would be d
Dear Filip,
I believe that you may find interesting methods, insights and principles to get
you going in the following paper:
Wu et al.
Transforming binding affinities from three dimensions to two with application
to cadherin clustering.
Nature. 2011 Jul 27;475(7357):510-3
doi: 10.1038/nature10
Dear all,
please follow the link
http://www.hecra.gr/vacancies/21_6.pdf
for a posdoctoral position in Organic Synthesis at the Department of
Biochemistry and Biotechnology, University of Thessaly.
Demetres
--
---
Dr. Demetres D. Leonidas
Associat
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