Hi Reza.
Clearly nobody needs to know anything about what protein you are
specifically working on; that being said, in order to avoid a potentially
endless email string of expert advices, please include everything
detail-wise regarding your expression system, culture conditions,
induction, and lysi
Dear All,
In coot when I try to build a peptide by baton method, I find the starting
point of the baton starts from somewhere in the sidechain rather than from the
Calpha position. In addition, when I try to changing the starting residue by
Baton-build params, the starting point of the Baton d
Question: you're taking a 3-ml equivalent out of 500 ml culture, and
processing it as if it was a 3ml culture? Or are you basing the result on
processing the entire 500ml?
Reason I ask this is simply to make sure your extraction/purification
timing is the same in both cases. It matters!
Assuming
Dear Reza,
It sounds to me like an aeration issue. I don't of course know how the 3 ml
culture is grown, but if say the small culture is less perfectly aerated
and slightly anaerobic, slower growth would mean slower metabolism and
slower protein production as well so things do not build up so easi
Hi,
We can express quite a bit of soluble protein when growing 3ml cultures.
However, the protein becomes insoluble (inclusion bodies) when we scale up to
500ml cultures. Has anyone experienced such a problem, and found a solution to
it? Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Pr
Dear Charles,BLEND assumes data to be continuous sweeps, i.e. they should not
include gaps. A valid data set,for example, could go from image 1 to image 100;
an invalid one from 1 to 20 and, say, 22 to 100 - forsome reason image 21 has
gone missing.
This can be annoying, I know, and, indeed, a f
when I use BLEND to analyze multiple mtz files, some are reported as
invalid datasets.
I processed these datasets in the same way, XDS and then POINTLESS. I am
looking at the detail of the processing. Meanwhile, I would like to know
what others could make these datasets invalid as judged by BLEND
Hi all,
I should mention 2D-GraLab which is a nice program (you must register to
download it) to display in 2D and analyze (a little bit as LigPlot)
interactions between two chains within a structure.
I have verified the data outputs for several interacting partners using
a different program.
Has anyone interfaced an image plate detector to a Bruker Microstar micro
focus with 3-axis goniometer? We have a Bruker AXS Proteum/R 6000 with a
smart 6000 CCD detector, but the CCD detector has died. I am wondering if
it is possible to replace the CCD detector with an image plate detector?
The
Website: http://www.psi.ch/lbr/
Technical Assistant
Membrane Protein Production, Purification and Crystallisation
Laboratory of Biomolecular Research – Schertler Lab
Paul Scherrer Institute, Switzerland
Description
The Paul Scherrer Institute PSI is the largest research centre for natural an
Dear All
Instruct and BioStruct-X need your help to learn from your experience of
accessing structural biology research infrastructure in the last few years
using Instruct or any other access route. The information you provide will help
us to improve the access we provide and plan for future ch
Dear All,
when I use BLEND to analyze XDS-POINTLESS processed mtz files, some are
reported as invalid datasets. Do you guys have some suggestions on what
could be wrong with the datasets?
I processed these datasets in the same way, XDS and then POINTLESS. I am
looking the detail of the processing
Hi Smith,
Both PDB and MTZ have records on their headers to specify the cell
dimensions and space group. And for an MTZ, once the cell dimension and
space group are fixed, its coordinate origins can also be fixed. For a PDB,
its "CRYST1" record specifies its unit cell dimensions and space group.
Dear Smith,
Coot calculates electronic map from data columns in the mtz file. If a
correct model (atomic coordinates) in a PDB file is generated from the mtz file
(Model building). This mode (PDB file) will " fit " the mtz file.
Yours
Sincerely!
Lu Zuokun
--
卢作焜
南开大学新生物站A202
在 2015-0
As this is a ccp4 bb we should mention the jsPISA server which is at
http://www.ccp4.ac.uk/pisa/
This is a very nice implementation of the PISA approach.
Another approach is to use the Chimera clash finding approach
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html
A 1-year crystallography postdoctoral position is available at King’s College
London (Sutton, McDonnell & Beavil) to work on small-molecule inhibitors of a
protein-protein interaction, as part of an ongoing collaboration with an
industrial partner.
Please see: https://www.hirewire.co.uk/HE/106
On 03/19/2015 07:20 AM, Smith Liu wrote:
Suppose I have a PDB file and a mtz file (PDB file from protein A, mtz
file from protein B, which is a homology protein of protein A) which
are not from the same refinment (thus not fit automatically in Coot),
will you please tell me what modification I
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