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Saturday, 21 November 2020

Shake it like a polaroid picture: MD in pyrosetta

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> This blog post has been unfinished for two years. So I am posting in the hopes it will spur me to finish it. The score of a pose reflec...
Sunday, 1 November 2020

Remote notebooks and Jupyter themes

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Jupyter notebooks are great. PyCharm is great for writing a module, but Jupyter notebook let's you test snippets of code really easily. ...
Saturday, 31 October 2020

XML to Pyrosetta: EvolutionaryDynamicsMover as an example

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In the previous post I discuss the strategies to use a Pyrosetta class when the documentation lets you down. One topic discussed was the co...
2 comments:
Tuesday, 27 October 2020

Pyrosetta scripting without a manual

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I got recently asked how to figure out how to write a Pyrosetta script when there is no example. This is definitely the biggest weakness...
Friday, 9 October 2020

The Freedom unit for molar energy: the foot-pound-force per pound-mole

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In computational biochemistry the most commonly used unit is molar energy. The SI unit is kJ/mol (kilojoule per mole), but kcal/mol is also ...
Wednesday, 7 October 2020

Rosetta/Pyrosetta on a cluster or in the cloud

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Due to licensing Rosetta and Pyrosetta cannot be installed via apt-get/pip but has to be downloaded from the Rosetta Commons website. This m...
2 comments:
Monday, 17 August 2020

5-hydroxytryptophan biosynthesis

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  I was intrigued by a recent article in the journal Chem ( link )  entitled "Creation of Bacterial Cells with 5-hydroxytryptophan as a...