Use elbow.builder with SMILES strings
From OS X Scientific Computing
Contents |
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Setting it up
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Install Phenix
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Create a SMILES string for your molecule
SMILES stands for "simplified molecular input line entry specification"
Simple examples:
- Ethanol: CCO
- Cyclohexane: C1CCCCC1
- Benzene: c1ccccc1
For more involved molecules, or to learn the language interactively, try a Java Molecular Editor
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Draw the molecule in the JME
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Calculate Properties
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Copy the SMILES string
eg: O=C(Oc3ccc(c1cc(NS(=O)(=O)O)c(Cl)cc1c2cccc(C(O)(O)O)c2)cc3Br)C4CC4
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Run the Calculation as a single unix command
eg:
elbow.builder --opt --smiles="O=C(Oc3ccc(c1cc(NS(=O)(=O)O)c(Cl)cc1c2cccc(C(O)(O)O)c2)cc3Br)C4CC4"
Note the use of double-quotes to protect the special characters like parentheses.
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View the result
eg:
pymol $(ls -t *.pdb | head -n 1 )
