Fabry:Structure-based mutation analysis/Journal

Fabry Disease » Structure-based mutation analysis  » Journal

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Vizualisation

The mapping of all SNPs was done with the bash script map_mark_positions.sh

bash map_mark_positions.sh

It creates the script map.pml, which can be loaded in pymol. The resulting 30 png pictures were merged into an animated gif with convert.

convert -delay 80 *.png map.gif

Create mutation

The mutated sequences that were used as input for SCWRL were generated by the script scwrl_generate_mutation_sequences.sh which again uses the perl script scwrl_mutate_sequence.pl for the actual mutation change. Afterwards, the models were calculated using scwrl_calculate_models.sh. The available options for SCWRL can be found here.

bash scwrl_generate_mutation_sequences.sh
bash scwrl_calculate_models.sh

An additional run without any mutation was also done.

Scwrl4 -h -s scwrl/sequence.fasta -i 3S5Y_chainA_repaired.pdb -o wt.pdb > wt.log

foldX

ln -sf /opt/SS12-Practical/foldx/rotabase.txt
wget http://www.rcsb.org/pdb/files/3S5Y.pdb
perl ../repairPDB 3S5Y.pdb > 3S5Y_repaired.pdb 
/opt/SS12-Practical/foldx/FoldX.linux64 -runfile run.txt

Minimise

bash call_minimise.sh

Gromacs

bash gromacs_mutations.sh ../scwrl/models/*