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

junfeng liu jliu at nimr.mrc.ac.uk
Mon Feb 16 09:01:02 PST 2009

Hi Young-Jin,
For the second one you can try lower the scale factor of wxu and wxc  
from  default (1 and 0.5) .  Is it the first round to run phenix? If not 
better to go back and rerun it again.
See the manual for details:

And  for the first one |I have no  experience  on that and no idea at 
all. Hope other guys will  help you for that.
Good luck!
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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