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Young-Jin<br>
<br>
I'm sorry for the delay.<br>
<br>
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.<br>
<br>
phenix.ready_set model.pdb<br>
<br>
will generate a file model.updated.pdb which contains the hydrogens.
ReadySet! also performs some other tasks to prepare your model for
refinement.<br>
<br>
Nigel<br>
<br>
On 2/19/09 9:24 AM, Young-Jin Cho wrote:
<blockquote
cite="mid:107536787.3065041235064292611.JavaMail.root@zimbra-store-3.unet.brandeis.edu"
type="cite">
<pre wrap="">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" <a class="moz-txt-link-rfc2396E" href="mailto:NWMoriarty@lbl.gov"><NWMoriarty@lbl.gov></a>
To: "PHENIX user mailing list" <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
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:
</pre>
<blockquote type="cite">
<pre wrap="">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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</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
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 : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Web : CCI.LBL.gov</pre>
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