On 19 November 2015 at 14:55, Alain Oregioni <Alain.Oregioni@xxxxxxxxxxx>
wrote:
Hi Edward,
Thank you very much for your reply; I'm glad it's a simple error. I'll add
protons to the PDB.
If I may say, it would be nice to have a simple way of doing it in the
script, even roughly for a start: if it "works" with a sequence, it wouldn't
be worse to do it with a PDB without H (add any warning necessary in the
description).
If you'd like to try to hunt down the scientific publications that are
the base reference for the correct placement of protons, that would be
a great start for implementing it. I searched once but failed. But
that was under a time constraint, so I ended up using Molmol. I
didn't like what PyMOL said about its algorithm, it sounds incredibly
un-scientific:
"h_add uses a primitive algorithm to add hydrogens onto a
molecule.", from http://pymolwiki.org/index.php/H_Add
It would be good to have a structure.attach_protons or
structure.add_protons user function so that everything can be
performed in the script. However in some cases (for example, say in
non-planar aromatic rings), a proper QM, QM/MM, or force field
optimisation may be required for accurate placement.
Hopefully, things will go smoothly for me from now on...
Well if it doesn't, don't hesitate to ask here. The mailing list
archives are also an incredibly useful reference:
http://www.nmr-relax.com/communication.html#mailing-lists
The amount of content archived - with both questions and answers - is huge!
This mailing list is very useful. keep it alive!
It's an open source project, so it can never really die ;) If you
like the mailing lists, maybe you'd find value in signing up for the
wiki as well ( http://wiki.nmr-relax.com ). Creating or expanding
articles, or documenting what you do in tutorials can be quite useful
for truly understanding the concepts. For example a new article on
adding protons to a 3D structure might help with the above ideas.
Regards,
Edward
Re: model free analysis: spin deselection problem