[phenixbb] phenix.ready_set hydrogens not compatable with coot library

Jovine Luca luca.jovine at ki.se
Mon Aug 23 09:11:46 PDT 2010

Hi Pavel:

>> This is absolutely true but, how about adding an option that would allow to (also) output a PDB version 2-formatted coordinate file at the end of a phenix.refine run? That way, one could read it directly into Coot for further model building, without hydrogens "exploding" at the first touch...
> I guess (not entirely sure) that if you use a recent Coot version then you shouldn't have problems with hydrogens. At least they don't fly away at the first touch. I just tried myself.

Well, I have the latest Fink version for OS X (0.6.2-pre-1-65), and they definitely do fly on my machine! Have you tried regularizing a Tyr residue, for example?

> Also, only a few gurus know about PDB format versions (2 or 3). Most of people will get confused seeing two PDB files at the end of refinement run, and they will flood us with questions about the differences between these two files and why and so on ... So I would just stick to the latest and wait a bit when the others adjust.
> Actually, phenix.reduce can output v2 formatted PDB. I guess it is "-OLDpdb" keyword. So if you really like to stick to the older format you can.

Yeah, sure, no big deal.

>> BTW, I think I already brought this up some time ago, but an option to output coordinate/map coefficients not only at the end of the refinement run, but also at the end of every intermediate macro cycle, would also be an useful addition to have.
> I'm wondering why? Imagine you refine a huge model and do 20 macro-cycles... You will get a bunch of huge files...

True, but occasionally one gets a quite clear "minimum" at - say - cycle 7... and then you have to re-run the whole thing again. Also, in this case, it's not a problem to just fire un another job... but if one would have this feature as an optional switch (off by default), it wouldn't hurt either. No?

Best, Luca

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