now: suggestions!
One idea: we should start by running a large language model on the complete
archive of Holton posts to the CCP4BB list.
...dave case
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xplicit solvent (water + ions). Fairly good results can also be obtained
using a generalized Born implicit solvent model. You should not expect to
get useful results with just the RNA coordinates alone.
...dave case
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ributions can improve things, but so far not by a lot. And the
(current?) restriction to high-resolution data sets is a pretty severe
limitation. But having a few people exploring the supercell idea seems
worthwhile, and I'm happy to share ideas (and code)
) often needs to be considered as well.
dave case
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On Fri, May 28, 2021, Hughes, Jonathan wrote:
if you just see the B factor as a number, ok, you can do the √ in your
head, but if it's visualized as in pymol/putty larger uncertainties become
exaggerated – which is another word for "misrepresented".
Two points that haven't yet been raised:
1.
On Fri, May 21, 2021, Fred Vellieux wrote:
CHARMM bulletin board similar to CCP4BB ?
The discussion site is called a "forum" in CHARMM-lingo. Try visiting
https://www.charmm.org/.
Note also the CHARMM-GUI (under Tools), which can be of considerable help in
setting up a system.
...dac
#
a ligand. One can hope that such usage will decline as
standard-conformance becomes more widespread.
dave case
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be long dead before the current PDB
format really goes away. [And I think that includes those just entering
the field.]
...dave case
On Thu, Dec 20, 2012, Phil Evans wrote:
> … is 20.12.2012
No, it's actually 12.20.2012, kind of a palindrome.
>
> Happy Christmas everyone!
And Merry Christmas to those on the left side of the pond!
...dac
so poorly.
...dave case
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