Dear Jorge,
It sounds like you want to estimate the 'pitch' parameter of a coiled coil.
You can extract that information from the structure using TWISTER program,
a server is available here:
https://pharm.kuleuven.be/apps/biocryst/twister.php
The alpha-helical chains need to be in-register, i.e. t
Gert,
There is nothing wrong with suggesting 45 softwares, as one of those may
do exactly what a person needs and save loads of time.
Besides, comparing protein structures locally need not involve any
superposition method. I would say comparing torsion angles/distances
between atoms is a mor
Have a look at local distance difference
test.https://swissmodel.expasy.org/lddt/
It's superposition-free and compares local atomic environment only. You will be
able to see unusually different regions from the output.
I am not aware of a similar structure comparison method that would also take
Hi Vikram,
Try Buccaneer, it works much better at such resolution than Arp/Warp.
Launch it several times with different parameters (e.g. use original
structure as seed/initial/nothing), then open the results together and
merge the pieces that look best and have lowest b-factors. Use Buster
fo
Hi Folmer,
> I was hoping to see what kind of science was behind the computer program that
> generated the unique papers.
Combinatorics in this case. The article was pre-written, he just replaced some
names.
Typically for hard science texts you would use a formal grammar with random
productio
Hi JI,
Just FYI: we have a working setup of Nvidia 3D Vision on Quadro FX 3700 with
Acer GD235HZ under Ubuntu 12.
Quadro FX 3450/4000 was also tested (not officially supported by NVidia, but
has all the capabilities) - although it works in principle, there was an
annoying flickering effect I c
