Nigel,
Have you had a chance to look at my pdb files? Anyway, I was suggested to use molprobity website and I could get hydrogen added pdb file from there.
I am inclined to think it is another bug of phenix though, which I thought was solved from new version. Just let me know what the problem is.
Then have a good day!
Young-Jin
----- Original Message -----
From: "Nigel W Moriarty"
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 : [email protected] Web : CCI.LBL.gov _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb -- Postdoctoral Fellow, Kern Lab Biochemistry Department/HHMI Brandeis University