davidchern / xtalkit

Some kits for bioinformatics and crystallographic computation

xtalkit

clustalx.py

A convenient toolkit for directly coloring the output of clustalw2 (.aln file) on console, so you don't have to use a website for visualizing the result of sequence alignment.

Run on Python 2.7 under Linux and Mac OS (Windows not supported), probably on Python 3.x also, yet not tested.

Requirement

You need to have CCP4 installed, which includes a copy of clustalw2.

Usage

Just put clustalx.py to a convenient path, e.g, /usr/local/bin, and run

chmod +x /usr/local/bin/clustalx.py

Then, prepare a fasta file for sequence alignment, and just run

clustalx.py [-k | --keep-aln-file] <fasta_file>

You will see the colored result of sequence alignment. Enjoy!

paref.py - parallel model refinement using phenix.refine

A toolkit for running multiple jobs of phenix.refine in parallel, especially useful when doing simulated annealing. It can automatically pick up the best result amongst all the jobs (based on lowest R-free values).

Requirement

You need to have Phenix properly installed.

Usage

First put paref.py into a convenient path, e.g. /usr/local/bin, then run

chmod +x /usr/local/bin/paref.py

Prepare a param.def file for the running of phenix.refine, and just run as following,

paref.py [options] param.{def,eff}

Options:
  --jobs=          | -j : number of jobs, default is 4.
  --make-all-seeds | -a : make all seeds, default is to keep the first one.
  --help           | -h : show this help information.
  more options can be configured in `~/.paref.yaml'.

You can specify number of jobs, whether or not to use all CPUs, whether or not to make all random seeds, etc.