Pierre,
For what its worth, I just tried using "Real Space Refine Zone" on something I am working on now
(2.8A resolution, in coot 0.5.2, build 1691). With the "LINKR" record generated by REFMAC5, my
glycan slithers down into the protein density. Similarly, using "Regularize Zone" does not en
Hi Damian,
I have used both Coot and Refmac for glycan modelling/refinement in the past,
last time was 2 or 3 years ago. They both behaved correctly for me.
To get the correct behaviour, you must have the correct LINK cards in the
header. At the time, the Chemical ID BMA did not exist in the PD
Since there are some crystallographers who also do electrophysiology / patch
clamping, I thought it might be possible that there is a homologous BB for
those techniques, and that a posting here would be a good means to find
such, i.e.,
Is anybody aware of a BB similar (or greater) in vivacity
I am also having problems with the branching.
The fucose linked to the first NAG being linked to the second NAG of the
carbohydrate chain.
So one has a linear chain NAG-FUC-NAG-MAN-MAN-MAN
instead of the FUC being a branch out from the first NAG. i.e. :
NAG-NAG-BMA-BMA
||
FUC MAN
H
There is no excuse for using MAN to mean both alpha and beta mannose.
It is easy to take a MAN-b-D.cif file and modify it to a BMA.cif. BMA
is already in the monomer library that comes with ccp4 (but I think it
does not have geometry descriptions), and the last time I checked, there
was not a
http://www.esrf.eu/Jobs/Research/CFR355
Subject: Kinetic Crystallography to Probe for Catalytic Mechanism and
Protein Loop Motions in Glycosyltransferases
General Framework: Glycosyltransferases are an enormous class of enzymes
responsible for the biosynthesis of oligosaccharides, polysacchar
For an "ideal" glycan, you could used a model from a high resolution
structure, or something that has been energy minimized, etc. Mostly I
find this helps in getting the sugars in about the right place (keeping
bond lengths and angles reasonable).
I perhaps could stand to fiddle more and mayb
Thanks! The 75 dpi fonts fixed it!
If I can chip into this somewhat sacrilegiously-named thread
1) I *would* use real-space refinement :), specifically Sphere
Refinement. You can dial down the
density weight if needed, of course.
2) the documentation on refining carbohydrates in Coot has recently been
updated
http://www.
Hi Martyn,
When it comes to micro-dialysis, you could check the following paper:
http://www.jbc.org/content/260/25/13580.full.pdf+html
(freely available, check in particular the appendix for the
micro-dialysis setup that was used, that was for heat-labile enterotoxin)
Fred.
PS I know this is
Thanks to those who replied.
The humour comes of course from a slight feeling that there is
some truth in the 'respectful' version. Proteins are wonderful subtle
machines so perhaps we should be careful and thoughtful when we expose them to
the
horrors of most crystallization conditions!
Which t
No, we haven't made that possible, largely because we can't see circumstances
where this would be desirable. However, you can get as close as you want to a
brute force search by changing the criteria for rescoring the results of the
fast search. If you include the command
FINAL TRA SELECT PER
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