[phenixbb] automatic linking vs .params file; hydrogens

Pavel Afonine pafonine at lbl.gov
Tue Jun 17 23:08:33 PDT 2014

Hi Georg,

> when is it advantageous to use automatic linking over supplying a .params file with the link parameters defined to refine links?
I'm sure Nigel will reply with the best answer.
What I can say is that automatic linking links atoms based on a variety 
of guess-work and some (mostly arbitrary) cutoffs (like, for instance, 
if two atoms are close within 3A let's postulate they are covalently 
linked, etc etc). What you specify in parameter file is the instruction 
for the program to do exactly that: if the parameter file says there is 
a link between two atoms, the program must obey and create that link. If 
it does not, please report a bug.

> I thought that automatic linking will recognize the kind of link by itself and then look for the restraints itself. But it seems not to do,
> because it is not complaining that there are still hydrogens in the sugar moeity which should not be there after the link has formed.
> This brings me to my second questions. Is there a way to automatically remove the hydrogens which should not be there anymore after the bond has formed.  Or tell reduce that it should not add hydrogens at the link?
I might be wrong (Nigel to correct me), but I doubt H are removed 
automatically when necessary to form a link. So I would use inputs that 
are as close as possible to what you want, and also instruct the program 
about what you want, and then hope it does what you want. Again, if it 
doesn't, please report a bug.

Good luck!

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