The RCSB PDB is seeking a Scientific Software Developer with skills as a
seasoned, experienced bioinformatics programming professional and a broad
understanding of computational algorithms.
The incumbent will develop, implement, and maintain complex scientific and
web-based software systems for th
Dear CCP4 community,
We are expanding our Structural Biology group at Evotec and we have many
positions open in our Protein Science team.
If you are interested, please apply using this link:
https://evotecgroup.wd3.myworkdayjobs.com/en-US/Evotec_Career_Site/job/Abingdon/Mammalian-Expression-Scien
Hi,
on behalf of Dr. Di Xia, I am posting this interesting job opportunity:
We are looking for a young research scientist with a recent Ph.D. in structural
biology with training in cryo-EM/X-ray crystallography to join our Section of
Structural Biology of Membrane Proteins in the Laborator
Hi Nika,
- As Herman wrote, you should use common sense to interpret a polder map:
if the ligand is not there, this kind of map may show only bulk solvent. So
the appearance of some density in the area of the ligand does not "prove"
that the ligand is there. Also, map interpretation should be done
In reasonably compact format, the discussion topic is summarized in this
CCP4 weekend introduction
https://journals.iucr.org/d/issues/2013/02/00/wd5191/index.html
As far as the solvent exclusion self-deception via low occupancy goes, fig 2
here:
https://febs.onlinelibrary.wiley.com/doi/epdf/1
Dear Jon,
I don't think we have any disagreement. I just wanted to emphasize
that you should have your plan thought out at the start. You may have
decided that you will compare your ligands shape with your map using a
Real Space R Factor. If you don't like that number the fault isn't in
Hi Paul,
Am 25.11.20 um 17:14 schrieb Paul Emsley:
I have committed 30ec64cc9906a5f19142a87d88b522f6f65409fa which I
think/hope should fix the problem (undoing the breaking). Just to be
clear, this commit doesn't require that you have backed out
5043f6adbbbc5725149e6c53bbbc6a85f3c5e8af.
30e
Hi All,
How can a noob user do that? Will CCP4 release a patched Coot binary?
Pedro
Às 15:25 de 25/11/2020, Christian Becke escreveu:
Dear Paul,
Am 25.11.20 um 12:05 schrieb Paul Emsley:
On 23/11/2020 15:21, Pedro Matias wrote:
In the latest coot update (to 0.9.2) in CCP4 the quad-buffered
Dear Paul,
Am 25.11.20 um 12:05 schrieb Paul Emsley:
On 23/11/2020 15:21, Pedro Matias wrote:
In the latest coot update (to 0.9.2) in CCP4 the quad-buffered stereo
doesn't seem to work. The NVIDIA emitter turns on but the stereo
picture does not appear when the glasses are turned on. Strange
Dear Nika,
The question is about a Fo-Fc map and the replies have been focused on such
maps.
However, I question why you are bothering with Fo-Fc maps.
The ligand was soaked into the crystal. There is probably an isomorphous apo
data set available.
A [Fo(ligand complex) - Fo(apo)]*exp(alpha_apo
Dear All,
An ITN PhD position is currently available in my laboratory in the field of
drug discovery. Within the MepAnti ITN we aim to develop and test novel
anti-infectives targeting malaria, tuberculosis and other infectious
diseases. The ideal candidate will have Xray experience, but we are als
On 23/11/2020 15:21, Pedro Matias wrote:
In the latest coot update (to 0.9.2) in CCP4 the quad-buffered stereo doesn't seem to work. The NVIDIA
emitter turns on but the stereo picture does not appear when the glasses are turned on. Strangely enough,
the only coot update I can find in the updat
Hello Robbie,
Yes exactly, I agree. I thought that was what the poster faced: density with
insufficient detail and not extending sufficiently for the whole ligand.
To make the discussion thread more focussed a screenshot or two would assist
us.
Greetings,
John
Emeritus Professor John R Helliw
Hello,
I just tested some structural biology programs on my MacMini with M1 chip (base
model, MacOS 11.0.1). After installing Xcode command line tools 12.2 and
Xquartz 2.7.11, open source pymol 2.4.0 (via homebrew), coot 0.8.9.3 (W.
Scott's binary) and UCSF chimeraX 1.1 (official dmg) are all w
I’m with Dale on this, the scientifically prudent thing is to set the rules and
then play by them. Not to change the rules as you go. Of course, in a teaching
environment where you know the correct answer, it is good to be educational and
learn how to dig a bit more.
However, in a scientific se
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