A brief reflection on IDPs
Increasingly, people with a computer science background are analyzing the
data deposited in the Protein Data Bank. In the case of conformation
disorder analyses, they consider residues that are explicitly stated to be
disordered (the old REMAR 465 records). This is not
Hi,
1) maybe work on refining the protein structure first, so that your
residual maps improve in quality.
2) Maybe only part of the peptide is ordered? Can you assign part of the
sequence? Starting a bulky aromatic (e.g. W/Trip)?
3) do you have a way to QC your peptide? Is it still 11 residues in
Hi,
Sorry, I haven’t had time to read all the posts in this thread, but do people
think that these fancy new lightfield displays will be the preferred route for
3D visualization in the future?
For more information, see
https://www.arch.tamu.edu/app/uploads/2021/10/FoVI3D_DeepDrive.pdf
Has any
Hi Wulf,
As some folks indicated already: Quad-buffered Stereo using Nvidia
3DVision shutter glasses still works under Windows 11 - no need to
despair as long as you still have the proper monitor and shutter glasses...
Just checked it using a new PC with a cheap professional graphics card
(N
Hi Pavel,
Interesting! I have always been told that one should include only what could be
seen. In this scenario, I would model hydrogens only if I had a sub 1 A
resolution or if I had Neutron diffraction data. Thanks for the documentation.
All the best
__
Hi Clemens,
I have a workstation running under Rocky Linux 8 with a Nvidia RTX A4000
graphics card plus the bracket for the 3-pin mini-DIN connection. The
last Nvidia driver that both recognizes and activates the Nvidia 3D
Vision IR emitter is the 525 driver which can be installed from the
N
Just to clarify: Gnome never worked with 3D stereo in the past
(gnome-shell is incompatible with switching off compositing), which is
why is used XFCE. 3D stereo with Gnome works to my knowledge only under
Fedora and more recent Red Hat Enterprise Linux versions (or clones of
it). Unfortunately
Hi
It looks like the peptide is bound close to a 2_fold symmetry axis, which can
result in mistakes, so try to anchor your peptide registry using regions that
are away from this axis (turn symmetry on in COOT to make sure you dont build
it inside itself).
Other than, that its just a case of t
Hi Wim,
we had the problem with smeared/unreadable scroll-able menus in Coot
with activated 3D stereo both under Debian 11 and Rocky Linux 8 using
XFCE. This does not happen with Rocky Linux 8 using Gnome. I think, it
has something to do with a different way of switching to 3D stereo under
G
That is true. The MPNN is implemented in the RFdiffusion notebook with
validation via alphafold.
On Fri, Feb 28, 2025 at 8:28 PM Jurgen Bosch wrote:
> You need Protein MPNN, otherwise you’ll just get a poly-glycine chain
>
> Jürgen
> ___
> Jürgen Bosc
Greetings,
It's hard to disagree with this! Resolution, occupancies, and B factors
only indirectly suggest what's visible and what isn't — and they can be
especially difficult to interpret correctly for non-specialists. Perhaps a
local confidence measure — similar to pLDDT for predicted models — c
Hi Rafael,
This is progressively getting further off-topic, so we may consider
continuing this conversation off-list or under a different subject line.
You are correct that "one should include only what could be seen". However:
a) "What could be seen" is not always necessarily a hefty green blob
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