On Mon, Apr 01, 2024, James Holton wrote:
My question for the BB is: what would YOU do if you had $1e12 USD for
your science? No non-scientific proposals please. There are plenty of
other forums for those. This BB is about biological structural
science, so please stay on-topic. OK? And now
On Thu, Sep 21, 2023, Abhilasha Thakur wrote:
If anyone is using the AMBER OL3 force field kindly send it to me. I am
working on RNA str prediction.
I think the official source of OL3 parameters is here:
https://fch.upol.cz/ff_ol/
This will cite the correct references. OL3 is based on earli
On Tue, Mar 28, 2023, James Holton wrote:
Members of an ensemble spread out over a supercell are equivalent to a
conventional multi-conformer model, but only when it comes to the
density derived from the coordinate atoms alone. They are not the
same when it comes to bulk solvent and also not
On 11 Nov 2022, 19:46, Murpholino Peligro wrote:
Can hydrogens be added in a pH/pka-dependent manner? Something like this
(https://server.poissonboltzmann.org/) but get a pdb file ready for
phenix.refine/buster/refmac?
You might want to try http://newbiophysics.cs.vt.edu/H++/. It outputs an
u
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
#
On Sat, Feb 13, 2021, Nicholas Larsen wrote:
I hope this doesn't confuse the discussion, but my understanding was "UNK"
stood for "unknown" residue and this will cause errors.
UNK is a legitimate entry in the components.cif collection. It's name is
indeed "UNKNOWN", but it is of type "L-PEPTI
On Mon, Aug 05, 2013, Boaz Shaanan wrote:
> I teach many such students and it's fairly easy to explain to them where
> to look in the PDB for particular pieces of information relevant to the
> structure. I can't imagine how they'll cope with the cryptic mmCIF format.
For many purposes, it's not a
