[phenixbb] automatic linking vs .params file; hydrogens

Benjamin Stauch bs448c at gmail.com
Wed Jun 18 12:14:09 PDT 2014


I believe I had the same issue a couple of days ago (check the mailing list
archive for reference ..) -- I was introducing a Asn-NAG-NAG albeit not
using automatic but explicit linking (I can provide the necessary file if
needed) and I ran into trouble with hydrogens -- Phenix was deleting them
after linking, however b/c I had checked the "automatically add hydrogens"
option in the GUI it was giving me an error for unparametrised hydrogens.
So I had to make sure to UNcheck the add hydrogens box.



2014-06-18 8:08 GMT+02:00 Pavel Afonine <pafonine at lbl.gov>:

>  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!
> Pavel
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