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Hi Raja,<br>
<br>
this should work (the rightmost Zn is shifted one space left as
required by PDB format):<br>
<br>
ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00
16.89 Zn<br>
<br>
let me know if it doesn't.<br>
<br>
Pavel.<br>
<br>
<br>
On 5/26/09 1:52 PM, Raja Dey wrote:
<blockquote cite="mid:f9cebedb93a2.4a1bf414@usc.edu" type="cite">
<pre wrap="">Hi Pavel,
I enclosed the line below:
ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00 16.89 A Z
I also tried with
ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00 16.89 A Zn
None worked.
Raja
----- Original Message -----
From: Pavel Afonine <a class="moz-txt-link-rfc2396E" href="mailto:PAfonine@lbl.gov"><PAfonine@lbl.gov></a>
Date: Tuesday, May 26, 2009 12:40 pm
Subject: Re: [phenixbb] creating cif for Zn
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="">Hi Raja,
normally phenix.refine should recognize Zn atoms without any
problems
and you don't need run elbow for this. If it doesn't, that most
likely
means your PDB file is ill-formatted (for example, no element type
defined in 77(?) column). Could you please send me copy of the ATOM
line
from your PDB file containing Zn so I can tell what is wrong?
Pavel.
On 5/26/09 12:31 PM, Raja Dey wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear Friends,
I have Zn atoms in my pdb file. So, I think
</pre>
</blockquote>
<pre wrap="">I need to run elbow to create the cif otherwise refinement stops.
</pre>
<blockquote type="cite">
<pre wrap="">I did the following and got the error as follows:
phenix.elbow generate_easy_r4.pdb --do-all
-----------------------------------------------------------------
</pre>
</blockquote>
<pre wrap="">-------------
</pre>
<blockquote type="cite">
<pre wrap=""> electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.4 3
- Nigel W. Moriarty (<a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.Gov">NWMoriarty@LBL.Gov</a>)
-----------------------------------------------------------------
</pre>
</blockquote>
<pre wrap="">-------------
</pre>
<blockquote type="cite">
<pre wrap=""> Random number seed: 664322001
0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing
</pre>
</blockquote>
<pre wrap="">Parsing Parsing P
</pre>
<blockquote type="cite">
<pre wrap=""> No molecule read
Use --all-residues to view residues if this is a PDB file
Can anyone suggests at this point, what I should do?
Thanking you in advance...
Raja
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