Young-Jin

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 refinement.

Nigel

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" <[email protected]>
To: "PHENIX user mailing list" <[email protected]>
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
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