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Hi Jobi,<br>
<br>
I hope Jeff has helped you already. So just as a remark of how you
can quickly debug it...<br>
<br>
Just type this from your command line:<br>
<br>
phenix.pdb_atom_selection model.pdb "chain S and resid 501 and name
C7"<br>
<br>
and that will print the lines from PDB file that you have selected
with the above atoms selection syntax.<br>
<br>
Similarly do for another one:<br>
<br>
phenix.pdb_atom_selection model.pdb "<font size="3"><font
face="Times New Roman">chain A and resid 25 and name SG</font></font>"<br>
<br>
If it doesn't print anything or complaints, that means that either
your atom selection syntax is not right (which is NOT your case
since it appears to me correct), or simply you are trying to select
atoms that are NOT present in your PDB file (empty selection).<br>
<br>
Pavel.<br>
<br>
<br>
On 10/20/10 10:49 PM, Jobichen Chacko wrote:
<blockquote
cite="mid:AANLkTim4MF1N30oOMmsgPL0BY-8CWYS29NbbM1iUh0rO@mail.gmail.com"
type="cite">
<div class="MsoNormal" style="margin: 0in 0in 0pt;"> Dear All,<br>
I am trying to make a custom covalent bond with an inhibitor
compound and my protein. Plesae see the attached file for
restraints file. But phenix is returning this error. Please
help.</div>
<div class="MsoNormal" style="margin: 0in 0in 0pt;">Sorry: No atom
selected: 'chain S and resid 501 and name C7</div>
<div class="MsoNormal" style="margin: 0in 0in 0pt;"><br>
I am using version1.6-289</div>
<div class="MsoNormal" style="margin: 0in 0in 0pt;">Thanks.<br>
Jobi</div>
<div class="MsoNormal" style="margin: 0in 0in 0pt;"> </div>
<div class="MsoNormal" style="margin: 0in 0in 0pt;"><font
face="Times New Roman" size="3">refinement.geometry_restraints.edits
{</font></div>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font size="3"><font
face="Times New Roman"><span> </span>bond {</font></font></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font size="3"><font
face="Times New Roman"><span> </span>action = *add</font></font></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font size="3"><font
face="Times New Roman"><span> </span>atom_selection_1
= chain S and resid 501 and name C7</font></font></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font size="3"><font
face="Times New Roman"><span> </span>atom_selection_2
= chain A and resid 25 and name SG</font></font></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font size="3"><font
face="Times New Roman"><span> </span>distance_ideal =
2.35</font></font></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font size="3"><font
face="Times New Roman"><span> </span>sigma = 0.1</font></font></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font size="3"><font
face="Times New Roman"><span> </span>slack = None</font></font></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font size="3"><font
face="Times New Roman"><span> </span>}</font></font></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font
face="Times New Roman" size="3">}</font></p>
</blockquote>
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