Hi Daniel,
Apparently, no b-factors were assigned, or the CA positions in all states are
identical.
Here is a similar script, maybe that works better for you (uses “rmsf2b” from
PSICO):
run
https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/editing.py
fetch 1nmr, async=0
rmsf2
Hello,
I found in this repository http://muralab.org/~cmura/PyMOL/ an script
(average3d.py) to perform the sausage representation in PyMOL. Although it
works perfectly good with the pdbs given in the examples, I couldn't get
the same results for my molecule. After performing all the RMSD
calculati
Hi
I am not sure which method is being used by PyMOL but because the
algorithm uses a dot density term it is likely the Shrake & Rupley
algorithm also known as the rolling ball method. You should read the
FreeSASA article (freely available
https://f1000research.com/articles/5-189/v1 ). The author p
Thank you for your reply. With regard to the algorithm used, do you
have any idea which algorithm is used in the Pymol calculations? DSSP
is likely to be using the rolling ball method.
Regards.
On Thu, Apr 27, 2017 at 1:35 PM, Emilio Xavier Esposito
wrote:
> Hi
> The accuracy of the calculation
Hi
The accuracy of the calculation depends on the dot_density value (the
amount of sampling done) with 1 being the lowest quality and 4 being
the best quality. A dot_density value of 1 uses less computational
resources (time) than a dot_density of 4 because of the amount of
sampling performed to ca
