[phenixbb] 2 Wonderings: adding H atoms and overcoming overfitting problem

Young-Jin Cho yjcho at brandeis.edu
Mon Feb 16 08:34:54 PST 2009

my current wonderings are as below:
First, how can I add H atoms into nucleotide ligands in pdb file?
I did 'phenix.reduce model.pdb > model_h.pdb', but as I see it didn't add H's of sugar (1', 2', 3' 4' and 5').
Once I had this kind of problem before, I was suggested to use phenix.ready_set command but seemingly this does not work any longer with last version that I am using now. Also, is it possible to add H into phosphate group?

The second very general question is about getting over overfitting problem. My phenix runs gave me too much difference between R and Rfree about .7 w/o adding H atoms. I assume it came from water molecules because it(huge gap) just starts to happen after 1_bss stage. If anybody can suggest a good way to get over this problem, you will save my tremendous times and useless efforts.

Big thanks in advance,


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