Fabry:Structure-based mutation analysis/Journal
The mapping of all SNPs was done with the bash script 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
The mutations were introduced on the basis of an backbone independent rotamer library to show the difference to the backbone dependent library used in SCWRL. The pictures were created with the pymol scripts mutSingle.pml and surface.pml
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.
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
Afterwards the minimal energies were parsed from the logfiles and compared to the minimal energy of the wildtype.
The pictures were again created with pymol on the basis of the .pdb files created by SCWRL4 and the pymol script scwrl.pml
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
Again, the pictures were created with pymol on the basis of the .pdb files created by FoldX and the pymol script scwrl.pml
The energies were extracted with
Afterwards plots were created
and example pictures made with pymol its.pml
bash gromacs_mutations.sh ../scwrl/models/*