Dear colleagues,
I wanted to highlight a tenure track job that may appeal to structural
biologists, biochemists, and/or biophysicists. Happy to answer any questions
you may have.
Best,
Lauren
Vanderbilt University invites applications for a tenure-track, faculty position
in evolutionary
Hi Robbie
I also use them quite regularly (less so coordconv, although I do use it),
typically from the command line
Thanks, Alejandro
> On Aug 30, 2021, at 17:38, James Holton wrote:
>
> I use pdbset, coordconv and sftools a LOT. Usually for things no other
> programs do, like converting
I use pdbset, coordconv and sftools a LOT. Usually for things no other
programs do, like converting to fractional coordinates, and performing
math operations on mtz data. Always from command line scripts.
-James Holton
MAD Scientist
On 8/26/2021 3:29 AM, Robbie Joosten wrote:
Dear CCP4
Dear Eleanor,
Thanks for pointing out that CCP4 FreeRflag selects the test set in the highest
possible symmetry for the crystal class! I didn't know that.
The following sentences (which are somewhat difficult to understand for me) in
https://www.ccp4.ac.uk/html/freerflag.html appear to
Dear Robbie,
I don't use ccp4 regularly (since our structures are mainly small
molecule structures), but when I do, I often use pdbset. I use it to
remove het-atoms, or side chains, or water molecules, or reset the
B-value.
I also use sftools. I have a script for calculating Rcomplete with
Dear Andrew,
what I meant is "Everything else being equal, bad data result in a larger
Rfree-Rwork gap than good data". Of course the gap also depends on the
resolution, and other factors.
best wishes,
Kay
On Mon, 30 Aug 2021 16:59:12 +0100, Andrew Leslie - MRC LMB
wrote:
>Dear Kay and
Back to FreeR factors - Phenix, and I believe FreeRflag now select FreeRs
in the highest possible symmetry for the crystal class - eh P6/mmm for a
trigonal crystal, and expand the set to fill the actual space group. This
means the Free R assignment is suitable if later the crystal symmetry is
Dear Kay and Jon,
I cannot remember Ian Tickles original posting on this (assuming that it was
made to the bulletin board), but surely the resolution of the data is also a
very important factor in the danger of over-fitting. The lower the resolution,
the worse the experimental data to refined
Hi Jon,
generally I agree that the accuracy of the data is inversely related to the
danger of overfitting, and that selection in shells is not necessary.
But if twinning is suspected, as here, and/or a choice between high and low
symmetry spacegroup has to be made, one has to make sure that
Dear all,
The deadline for the the call for access to experimental facilities,
integrating protein production services from Instruct-ERIC facilities and
protein characterisation or quantification of interactions by the biophysics
facilities of iNEXT-Discovery, is approaching.
10th of
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