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> pip install -e .                                                                              (biotite-dev)
Obtaining file:///Users/alex/Documents/biotite
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  ERROR: Command errored out with exit status 1:
   command: /Users/alex/Documents/software/miniconda3/envs/biotite-dev/bin/python /Users/alex/Documents/software/miniconda3/envs/biotite-dev/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py get_requires_for_build_wheel /var/folders/17/bwqs57x94hqfddnbzbhc2gzr0000gn/T/tmp17py970l
       cwd: /Users/alex/Documents/biotite
  Complete output (98 lines):

  Error compiling Cython file:

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>A0A010ZQC5|IPR017736(10...447)|Beta-glucosidase
MTGPDQFPQFPPGFVWGVATASYQIEGAVTEDGRGPSVWDTFSHTPGRTHDGDTGDVADDHYHRYPEDLDLMAGLGVNAY
RFSIAWPRIQPTGEGPVNPAGLAFYDRLVDAMLAKGITPAATLYHWDLPQALEDKGGWTQRDIPHYFAEYTAAVADKLGD
RVGLWCTLNEPFIVTAFGYVLGVHAPGRQLFTDAFAVAHHQLLGHGLAVEALRAANVTGTIGVVNALAPVHPDSDDPADH
VAAGILDTLMNRTYTDPLLLGRYPEETPAVYAGADLSVVKDGDLSTISTPIDFFGVNFYNPHRVRAAAPEQFGTGPLNFE
TVEYPGVPTTAMGWPVVPEAFTELLTGLHERYGEKLPPIYITENGAAYDDEPGPDGRVRDDDRIAYLDRHLRAVHAAMAA
GADVRGYFCWSFLDNFEWAEGYQKRFGLVRVDYETLERTPKASYDWYRSVIALAAAVGP
>A0A011AHF0|IPR017736(5...433)|Beta-glucosidase
MHHLPQDFVWGVATAAYQIEGAVDVDGRSPSIWDTFGRVPGAIANGDTGDVACDHYHRWPEDLGLIRELGVDAYRFSVAW
PRVIPTGTGAVNAKGLAFYDRLVDELLAAGIRPFVTLYHWDLPQVLQDKGGWPARHTAEAFADYAAVVAGALGDRVTDWT

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How to contibute to an existing Git project

So you've been using some cool Python module and found yourself wanting to add some functionality that you've made in an ad hoc way in your notebooks. This tutorial will walk you through how to 1) get the official repository, 2) add your code, 3) create a merge request letting the maintainer know that your code is ready to be merged in and available for all to use.

Before you start

Check that you have git

Make sure you have git installed. You can check to see if it is installed by typing which git at the command line. If you don't have it installed, you can use sudo apt-get install git (Linux) or brew install git (macOS) to get a copy of this free software (if you are using macOS and you don't have Homebrew, definitely get it).

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# STOCKHOLM 1.0

#=GS 101m_A/1-154   DE [subseq from] mol:protein length:154  MYOGLOBIN
#=GS 1mtj_A/1-154   DE [subseq from] mol:protein length:154  MYOGLOBIN
#=GS 1mtk_A/1-154   DE [subseq from] mol:protein length:154  MYOGLOBIN
#=GS 1mym_A/1-154   DE [subseq from] mol:protein length:154  MYOGLOBIN
#=GS 1mti_A/1-154   DE [subseq from] mol:protein length:154  MYOGLOBIN
#=GS 109m_A/1-154   DE [subseq from] mol:protein length:154  MYOGLOBIN
#=GS 110m_A/1-154   DE [subseq from] mol:protein length:154  MYOGLOBIN
#=GS 111m_A/1-154   DE [subseq from] mol:protein length:154  MYOGLOBIN

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How to share your awesome PyRosetta and XML scripts with the Rosetta community

Tutorial by Alex Carlin (carlin@ucdavis.edu)

So you've been developing some awesome Rosetta protocols using PyRosetta and XML, and you want to share them with the community. That's awesome! This tutorial will walk you through how to 1) clone the official repository, 2) add your scripts, 3) create a pull request letting the rest of the community know that your scripts are available to be merged in.

Before you start

Make sure you have git installed. You can check to see if it is installed by typing which git at the command line. If you don't have it installed, you can use sudo apt-get install git (Linux) or brew install git (macOS) to get a copy of this free software.

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def get_energies_dataframe(pose, score_function, residues=[]):
    
    values = []
    labels = []
    
    data = []
    
    if len(residues) > 0:
        residue_set = residues
    else:

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How to install PacBio SMRTLink on an AWS instance

Launch and config an EC2 instance

m3.2xlarge (8 CPUs, X GB ram, 2 x 80GB SSD instance storage)

Copy your data files to the instance

scp -r -i aws.pem data_files ec2-user@54.89.153.29:

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Kunkel mutagenesis with in vitro template generation

This is an idea for a protocol for performing site-directed mutagenesis. The first step is generation of the ssDNA template. The second step is the mutagenesis.

Template preparation

Bacterial transformation and cultures

1. Transform pET29b(+) harboring your construct into Escherichia coli CJ236
2. Plate on chloramphenicol (25 ng/µL) and kanamycin (50 ug/µL) selection plates

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1. Install Anaconda Python

2. Add a features reporter moveer to your RosettaScript. Or, if you have already generated output scripts and wish to scroe them and report features, use a simple script like the following

<ROSETTASCRIPTS>
<SCOREFXNS>
  <t weights=talaris2014_cst.wts />
</SCOREFXNS>
<MOVERS>

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How to design mutagenic oligos for use in Kunkel mutagenesis

First, prepare your input FASTA file. The codons in the input file must be in frame and have a one to one correspondence with the amino acid sequence of your Rosetta model. Otherwise, the numbering will be off. Do not rely on the script to catch input errors. This simple script attempts a crude error check that randomly fails to detect errors 1/20th of the time does not attempt any checking of your input sequence, so please make sure it's correct ahead of time.

A good way to do this: translate your input file into amino acid sequence, then align with the sequence from your PDB structure (native) from Rosetta (you can save a FASTA file directly from PyMOL, just do save my_FASTA.fasta on the PyMOL command line to write a FASTA file called my_FASTA.fasta to the current working directory). Just make sure they are 100% identical before proceeding.

Here is an example input FASTA:

>BglB