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

Nigel W Moriarty NWMoriarty at lbl.gov
Tue Feb 17 08:29:05 PST 2009


Which version of PHENIX are you using?  If you send your files directly 
to me I'll determine what is happening.


On 2/16/09 8:34 AM, Young-Jin Cho wrote:
> Hi,
> 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,
> Young-Jin
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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