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

Nigel W Moriarty NWMoriarty at lbl.gov
Thu Feb 19 09:57:20 PST 2009


I'm sorry for the delay.

To add hydrogens you should use ReadySet!  which uses Reduce for the 
protein and RNA/DNA portions of your model.  For other molecules such as 
ligands it uses eLBOW.

phenix.ready_set model.pdb

will generate a file model.updated.pdb which contains the hydrogens.  
ReadySet! also performs some other tasks to prepare your model for 


On 2/19/09 9:24 AM, Young-Jin Cho wrote:
> 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" <NWMoriarty at lbl.gov>
> To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
> Sent: Tuesday, February 17, 2009 11:29:05 AM GMT -05:00 US/Canada Eastern
> Subject: Re: [pdbphenixbb] 2 Wonderings: adding H atoms and overcoming overfitting problem
> Young-Jin
> Which version of PHENIX are you using?  If you send your files directly 
> to me I'll determine what is happening.
> Nigel
> 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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