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
Dear All,
When we by Coot open the PDB fle and the mtz file from the same refinement, the
protein backbone (and the sidechains) and the electron density always fit
automatically. Will you please tell me the mechanism of the Coot how the PDB
file automatically fit the mtz file in its
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
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
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
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:
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
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
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
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
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.
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
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.
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
Dear All
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