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Raja<br>
<br>
<blockquote cite="mid:6d5080f7181d6.4bdd5929@usc.edu" type="cite">
<pre wrap="">
Actually I used 3 letter code for nucleotides in PHENIX refinement. Before submission to PDB I changed to DA, DC ....like this. Otherwise PDB deposition system can not recognize. Might be there is a way, so that I can avoid this hassle of changing this code for PDB deposition. Please tell me if I did anything wrong.
Thanks...
</pre>
</blockquote>
This is very interesting. In my previous email, I had mixed up the
codes AD, CD, GD, TD that the monomer library uses and the standard
codes that PDB uses, DA, DC, ... Ralf tells me that phenix.refine
recognises these latter codes so there is something else up with the
refinement.<br>
<br>
You should follow Pavel's advice and check the .geo file. It certainly
seems like the refinement has not converged.<br>
<br>
Nigel<br>
<blockquote cite="mid:6d5080f7181d6.4bdd5929@usc.edu" type="cite">
<pre wrap="">
Raja
----- Original Message -----
From: Nigel W Moriarty <a class="moz-txt-link-rfc2396E" href="mailto:NWMoriarty@lbl.gov"><NWMoriarty@lbl.gov></a>
Date: Sunday, May 2, 2010 9:43 am
Subject: Re: [phenixbb] Error in PDB Validation letter
To: PHENIX user mailing list <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
</pre>
<blockquote type="cite">
<pre wrap="">Raja
Regarding the BML compound. This code is already taken for 4-
BROMOPHENOL. You can look at it using
phenix.reel --chemical-components=BML
You can generate a new unused code thus
elbow.get_new_ligand_code
and one being with B thus
elbow.get_new_ligand_code B
Then the PDB with not compare you compound with the one currently
known as BML.
Regarding the deviations. The nucleotides denoted as DA, DC, DT,
... are not using the standard codes. This may mean that you
generated new restraints that are not as accurate as the standard
set in the restraints library. Either way, I suggest renaming the
residues to the standard codes and re-refining. This will use the
standard restraints and will likely approach the values mandated by
the PDB.
Nigel
On 4/30/10 12:37 PM, Raja Dey wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
I am getting two errors in pdb validation report as follows:
I think I need to use B-DNA constraint in the refinement. This is
</pre>
</blockquote>
<pre wrap="">a 2.4 A data. How can I do that in PHENIX in cammand line promt.
</pre>
<blockquote type="cite">
<pre wrap="">Another thing is, I have a small molecule in the complex, which I
</pre>
</blockquote>
<pre wrap="">called as BML. I think that's might be the problem. This is known
as BML210. What I should call this compound? Should I also give a
chain ID for this compound? See the errors given below.
</pre>
<blockquote type="cite">
<pre wrap=""> *** Covalent Angle Values:
The overall RMS deviation for covalent angles relative to the
</pre>
</blockquote>
<pre wrap="">standard dictionary is 1.4 degrees.
</pre>
<blockquote type="cite">
<pre wrap=""> The following table contains a list of the covalent bond angles
greater than 6 times standard deviation.
Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond
</pre>
</blockquote>
<pre wrap=""> Dictionary Standard
</pre>
<blockquote type="cite">
<pre wrap=""> Name ID Number Angle
</pre>
</blockquote>
<pre wrap=""> Value Deviation
</pre>
<blockquote type="cite">
<pre wrap="">-------------------------------------------------------------------
</pre>
</blockquote>
<pre wrap="">------------------------
</pre>
<blockquote type="cite">
<pre wrap=""> -4.8 DA E 1 C1' - C2' - C3' 97.6
</pre>
</blockquote>
<pre wrap=""> 102.4 0.8
</pre>
<blockquote type="cite">
<pre wrap=""> -5.8 DA E 2 C1' - C2' - C3' 96.6
</pre>
</blockquote>
<pre wrap=""> 102.4 0.8
</pre>
<blockquote type="cite">
<pre wrap=""> 3.3 DA E 2 N9 - C1' - O4' 111.6
</pre>
</blockquote>
<pre wrap=""> 108.3 0.3
</pre>
<blockquote type="cite">
<pre wrap=""> -5.0 DC E 5 N1 - C1' - O4' 103.0
</pre>
</blockquote>
<pre wrap=""> 108.0 0.7
</pre>
<blockquote type="cite">
<pre wrap=""> -5.1 DT E 6 C1' - C2' - C3' 97.3
</pre>
</blockquote>
<pre wrap=""> 102.4 0.8
</pre>
<blockquote type="cite">
<pre wrap=""> -6.7 DT E 8 C1' - O4' - C4' 103.4
</pre>
</blockquote>
<pre wrap=""> 110.1 1.0
</pre>
<blockquote type="cite">
<pre wrap=""> 2.3 DT E 8 N1 - C1' - O4' 110.6
</pre>
</blockquote>
<pre wrap=""> 108.3 0.3
</pre>
<blockquote type="cite">
<pre wrap=""> -4.5 DT E 11 N1 - C1' - O4' 103.5
</pre>
</blockquote>
<pre wrap=""> 108.0 0.7
</pre>
<blockquote type="cite">
<pre wrap=""> -6.1 DA F 2 C1' - C2' - C3' 96.3
</pre>
</blockquote>
<pre wrap=""> 102.4 0.8
</pre>
<blockquote type="cite">
<pre wrap=""> 3.0 DA F 2 N9 - C1' - O4' 111.3
</pre>
</blockquote>
<pre wrap=""> 108.3 0.3
</pre>
<blockquote type="cite">
<pre wrap=""> -5.3 DC F 5 N1 - C1' - O4' 102.7
</pre>
</blockquote>
<pre wrap=""> 108.0 0.7
</pre>
<blockquote type="cite">
<pre wrap=""> -4.9 DT F 6 C1' - C2' - C3' 97.5
</pre>
</blockquote>
<pre wrap=""> 102.4 0.8
</pre>
<blockquote type="cite">
<pre wrap=""> -4.5 DA F 10 N9 - C1' - O4' 103.5
</pre>
</blockquote>
<pre wrap=""> 108.0 0.7
</pre>
<blockquote type="cite">
<pre wrap=""> -7.8 DA F 11 N9 - C1' - O4' 100.2
</pre>
</blockquote>
<pre wrap=""> 108.0 0.7
</pre>
<blockquote type="cite">
<pre wrap="">
==> The following residues have extra atoms:
</pre>
</blockquote>
<pre wrap=""> RES MOD#C SEQ ATOMS
</pre>
<blockquote type="cite">
<pre wrap=""> BML( 100) N1 C10 C11 C12 C13 C14 C15
</pre>
</blockquote>
<pre wrap="">C16 C17 C18 C19 O2 N2 C20 N3
C7 C8 C9
</pre>
<blockquote type="cite">
<pre wrap="">
ERROR: dissociated residue(s):
BML 100
Raja _______________________________________________
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</pre>
</blockquote>
<pre wrap="">--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Fax : 510-486-5909 Web : CCI.LBL.gov
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</pre>
</blockquote>
<pre wrap=""><!---->_______________________________________________
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</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 Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Fax : 510-486-5909 Web : CCI.LBL.gov</pre>
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