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But you still have to rename your glycerol. Otherwise, we may not be
able to interpret your pdb correctly when you finally publish it.
Please always check from HICUP or CCP4 monomer library for the naming
(and you can get cif files from there, too).<br>
<br>
Engin<br>
<br>
On 6/12/09 5:55 AM, <a class="moz-txt-link-abbreviated" href="mailto:sbiswas2@ncsu.edu">sbiswas2@ncsu.edu</a> wrote:
<blockquote
cite="mid:49345.65.190.191.54.1244811332.squirrel@webmail.ncsu.edu"
type="cite">
<pre wrap="">Hi,
This was not necessary it just ran fine with the cif file.
thanks,
shya
</pre>
<blockquote type="cite">
<pre wrap="">Dear Shya,
So did you rename your glycerol? You have to do that.
See <a class="moz-txt-link-freetext" href="http://xray.bmc.uu.se/hicup/GOL/">http://xray.bmc.uu.se/hicup/GOL/</a> and <a class="moz-txt-link-freetext" href="http://xray.bmc.uu.se/hicup/GLC/">http://xray.bmc.uu.se/hicup/GLC/</a>
Best regards,
Folmer Fredslund
2009/6/11 <a class="moz-txt-link-rfc2396E" href="mailto:sbiswas2@ncsu.edu"><sbiswas2@ncsu.edu></a>:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Folmer and Pavel,
Thanks for your suggestions. Phenix readyset gave me only .eff and .pdb
file so I ran elbow which gave me the cif file as the output and this
runs
and refines fine now (just to let everyone know). Folmer, the molecule
was
glycerol and not glucose anyway the problem was the cif file which I
could
easily generate in elbow. Thanks
Shya
</pre>
<blockquote type="cite">
<pre wrap="">Dear Shya
2009/6/11 <a class="moz-txt-link-rfc2396E" href="mailto:sbiswas2@ncsu.edu"><sbiswas2@ncsu.edu></a>:
</pre>
<blockquote type="cite">
<pre wrap="">Hi all,
I tried running phenix refine with a pdb file refined in cns. This has
a
glycerol molecule in it. I got the following message:
Number of atoms with unknown nonbonded energy type symbols: 42
"ATOM 6921 OAA GLC J 1 .*.J "
"ATOM 6922 CAD GLC J 1 .*.J "
"ATOM 6923 CAF GLC J 1 .*.J "
"ATOM 6924 OAC GLC J 1 .*.J "
"ATOM 6925 CAE GLC J 1 .*.J "
"ATOM 6926 OAB GLC J 1 .*.J "
"ATOM 6927 OAA GLC J 2 .*.J "
"ATOM 6928 CAD GLC J 2 .*.J "
"ATOM 6929 CAF GLC J 2 .*.J "
"ATOM 6930 OAC GLC J 2 .*.J "
</pre>
</blockquote>
<pre wrap="">First of all, glycerol should be called GOL not GLC. Do you mean
glucose ?
</pre>
<blockquote type="cite">
<pre wrap=""> ... (remaining 32 not shown)
Time building chain proxies: 11.79, per 1000 atoms: 1.69
Sorry: Fatal problems interpreting PDB file:
Number of atoms with unknown scattering type symbols: 42
Number of atoms with unknown nonbonded energy type symbols: 42
Does anyone know how to resolve this
thanks,
Shya
</pre>
</blockquote>
<pre wrap="">You need a cif file for the extra molecule. Can be found at eg. the
HICup server (<a class="moz-txt-link-freetext" href="http://xray.bmc.uu.se/hicup/">http://xray.bmc.uu.se/hicup/</a>)
Best regards,
Folmer Fredslund
</pre>
<blockquote type="cite">
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