Dear Phenix.BB,<br clear="all"><br>I wrote a mail earlier about some problems I had with phenix.elbow but it didn&#39;t seem to get through. I&#39;ve solved two of the problems now but also found a new one so I&#39;ll try posting again.<br>
When you set the --xyz option along with --clean then your .xyz file is deleted. Of course the easy solution is simply to not use --clean but I imagine that it is a minor bug since it doesn&#39;t happen with --tripos.<br>
Secondly I have a slightly larger problem. When an isoSMILES with more than one molecule is inputted then phenix.elbow joins them up to a single molecule (or places them so closely that all programs, including phenix.elbow, interprets them as one molecule when converting to a format such as mol2 with explicit bonds).<br>
For an example try<br>phenix.elbow --output=009_3085017 --write_hydrogens=false --overwrite --clean --tripos --smiles=&#39;C=CCN.C1C(O1)CCl&#39;<br>The period is supposed to designate two seperate molecules. Remember to use elbow.become_expert before running that line.<br>
<br>I hope someone can help me.<br><br>Sincerely,<br>-- <br>Morten K Grøftehauge<br>PhD student<br>Department of Molecular Biology<br>Gustav Wieds Vej 10 C<br>8000 Aarhus C - Denmark<br>Phone: +45 89 42 52 61<br>Fax: +45 86 12 31 78<br>
<a href="http://www.bioxray.dk">www.bioxray.dk</a><br><br>