[phenixbb] phenix.elbow

Morten Grøftehauge morteng at bioxray.dk
Mon May 19 10:00:43 PDT 2008

Dear Phenix.BB,

I wrote a mail earlier about some problems I had with phenix.elbow but it
didn't seem to get through. I've solved two of the problems now but also
found a new one so I'll try posting again.
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't happen with --tripos.
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).
For an example try
phenix.elbow --output=009_3085017 --write_hydrogens=false --overwrite
--clean --tripos --smiles='C=CCN.C1C(O1)CCl'
The period is supposed to designate two seperate molecules. Remember to use
elbow.become_expert before running that line.

I hope someone can help me.

Morten K Grøftehauge
PhD student
Department of Molecular Biology
Gustav Wieds Vej 10 C
8000 Aarhus C - Denmark
Phone: +45 89 42 52 61
Fax: +45 86 12 31 78
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