[phenixbb] tools to obtain ADP?

Pavel Afonine pafonine at lbl.gov
Wed Apr 6 18:32:44 PDT 2011

Hi Jason,

> It sounds doable. One minor point is that for ligand, phenix.pdbtools 
> needs restrain file. For ADP statistics, it seems asking a bit too much.

naively it may seem too much. But when you do selection on your model: 
for example, select certain protein atoms, water, ions, ligands, etc..  
the selection machinery needs to know what is what (at the very deep 
basic level), and obviously the PDB file alone is not enough of source 
of such information, therefore the library is needed. So if your PDB 
file contains a ligand that PHENIX "doesn't know", then you need to 
define it first before requesting any manipulation on it.

Your are right, you don't need it for ADP statistics, but in my example 
I was doing selection on a PDB file, so if you want to repeat anything 
similar your need a CIF file for your ligand that is strange to PHENIX.

Good luck,

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