Dear all
Gentle reminder about the deadline of tonight for statements of support for two
MX beamline projects at Diamond Light Source as part of the Diamond II upgrade
programme:
* A major upgrade (KMX) of I24 will enhance its microfocus capability and
extend further its serial
Dear all - if you see imaging cellular systems/ tissues organs at subcellular
resolutions as key to your research questions then please do take a few minutes
to add your support to our proposal for a dedicated bioimaging beamline at
diamond for just this! - the beamline will take advantage of
Hello,
I have a question about protein-ligand, of which ligand displays an ambiguous
electron density. I am solving a structure of protein with ligand which was
obtained via soaking. Structural characteristics indicate the ligand is present
however the electron density is quite vague and too
Dear Nika,
A tool I am gaining experience with, but for a challenge like you describe, may
help:-
In Coot>Calculate you see “Blurring/Sharpening tool”. You are presented with a
choice of electron density map (here you would select your Fo-Fc). There is
then a slider tool, to the left and to
Hello Dale,
Well, warming to your theme, I start with a trust in Coot before a new project.
Secondly, Coot’s blurring and sharpening tool is tethered directly to one’s
measured diffraction data.
Thirdly, scrutinising it at a sigma level above 5, Coot’s default, is certainly
not the same as
> On 11 Nov 2020, at 21:04, Alwyn Jones wrote:
>
> A greater concern may be lack of support for OpenGL/GLUT
Indeed, big concern.
Probably no other choice than switching to MetalGL :
https://www.raywenderlich.com/9211-moving-from-opengl-to-metal
Hi,
To me, this sounds like a very dangerous way to use this tool decide
if a ligand has bound. I would be very reluctant to modify my map with
a range of arbitrary parameters until it looked like what I wanted to
see. The sharpening and blurring of this tool is not guided or limited
by
Another idea - you dont mention resolution., but possibly the ligand is
very wobbly, and appropriate B values would range widely. Some refinement
defaults restrain the whole "residue" B factors quite tightly to a mean
value. There are ways to relax Bfactor restraints but you will have to read
the
Hi Nika,
A couple of other things you could try to improve maps to add to what the
others have suggested. One, I am assuming that you are refining the
occupancy of the ligand, but if not, that should reduce the negative
density? 2. Since you mention soaking the ligand, do you have a good
X-ray
Hi Nika,
Here you need some common sense. The green density in you polder map may just
be the bulk solvent that was removed from the model to generate the polder map.
In this case you have to use common sense and ask yourself a couple of
questions:
* Is the density really from the ligand,
Hello, I was wondering if you are refining the ligand occupancy. Eleanor
mentioned resolution which is important here. If it's good enough, occupancy
refinement of the ligand or the fragment will clean the map up, assuming the
occupancy is much less than one. Sorry, if I'm just saying the
An Assistant or Associate Professor position has opened in the Department of
Biochemistry at Université de Montréal:
https://www.umontreal.ca/public/www/documents/offres_emploi_profs/MED_11-20_8_Biochemistry.pdf
Enquiries and applications to:
Lorraine Bidégaré Charette
Postdoctoral position in drug discovery
An opening is available in the drug discovery laboratory of Dr. Stephen Fesik
for a post-doc in the field of protein x-ray crystallography. Responsibilities
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crystallography
Hello Dale, the statistical rigour you describe is, of course, excellent, but
in a learning environment, if someone gets a negative result, you have to go
into overdrive to check that everything has been done correctly, since there is
a fair chance that human error is the cause. It may be a
On 25/11/2020 03:24, Cheng Zhang wrote:
This question must have been asked before
Correct.
but I couldn't find a good answer online.
the jiscmail archive is a terrible system for archiving our collective
knowledge. There should be a better way.
I work on a cryo-EM structure with one
Hi everyone,
This question must have been asked before but I couldn't find a good answer
online.
I work on a cryo-EM structure with one serine residue covalently linked
with a lipid molecule. The map for the lipid moiety was there but not good
enough to unambiguously place each atom. I tried to
Hello, I think this thread from a few months ago will help.
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2007=CCP4BB=0=49210
Best wishes, Jon Cooper
Original Message
On 25 Nov 2020, 03:24, Cheng Zhang wrote:
> Hi everyone,
>
> This question must have been asked before
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