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Monday, 8 June 2020

Love thy neighbours, but select them with caution

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In Rosetta NeighborhoodResidueSelector behaves differently than PyMOL's expand selector and it is good to be aware of it. Namely, in P...
Sunday, 19 April 2020

How to set up an electron density scorefunction in Pyrosetta

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Energy minimising structures in Rosetta/Pyrosetta is essential to avoid artifactual results. Say a mutation is introduced and in the protoco...
Wednesday, 18 March 2020

Atom names purely in RDKit

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For some applications, such as PyMOL scripts or Rosetta, atom names are really important, say CA is the standard name for the α-carbon. Exa...
Friday, 21 February 2020

Working around segmentation faults of pyrosetta: threads & processes

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Rosetta often does not die gracefully. Pyrosetta is the same. If the starting template is not great segmentation faults will result in the...
Wednesday, 12 February 2020

Guess bond order in Rdkit by number of bound atoms

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Some compChem/Biochem programs do not care about bond order and strip them, which is rather frustrating. Ligands in random PDB files witho...
1 comment:
Sunday, 15 December 2019

What-if: Biosynthesis of deazaguanine

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7-deazaguanine is an analogue of guanine that has a carbon instead of a nitrogen. This molecule that is not made in nature, but many subst...
2 comments:
Saturday, 30 November 2019

Convert Python docstrings to GitHub markdown readmes

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This is suited for very small projects were read-the-docs is way overkill, however for most project that will be more suited — see how-to po...