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

Pavel Afonine pafonine at lbl.gov
Mon Aug 23 09:03:28 PDT 2010

  Hi Luca,

> 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.

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.

> 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...

Actually, if you run phenix.refine from the GUI, you can interactively 
see how model and map changes during refinement. It's pretty cool.


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