Hi. My colleagues Kresten Lindorff-Larsen and Amelie Stein kindly helped me find some references:
http://zhanglab.ccmb.med.umich.edu/HAAD/ http://zhanglab.ccmb.med.umich.edu/papers/2009_7.pdf Fortran code: http://zhanglab.ccmb.med.umich.edu/HAAD/haad.f90 http://kinemage.biochem.duke.edu/software/reduce.php http://kinemage.biochem.duke.edu/software/readme.reduce.html http://kinemage.biochem.duke.edu/php/downlode.php?filename=/downloads/PDFs/1999WordJMB285b.pdf I don't know the license of the programs, and if they should/could be implemented in relax efficiently by running the code as external program in the respectively software environments. Best Troels 2015-11-19 15:14 GMT+01:00 Edward d'Auvergne <edw...@nmr-relax.com>: > On 19 November 2015 at 14:55, Alain Oregioni <alain.oregi...@crick.ac.uk> > 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 > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-users mailing list > relax-users@gna.org > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-users > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
