XtalTransforms

Code that will perform crystallographic transformations on coordinates. Uses data from a RCSB PDB entry and coordinates in the CHARMM coordinate file. This code has NOT been thoroughly tested and will likely not work for all PDB structures.

Generate Coordinates for Unit Cell and Super Cell

0.) Configure

• Adjust the output file names in the driver file

1.) Compile

./compile.sh

OR

mkdir build
cd build/
cmake ..
make -j

2.) Run the code

• For this example you can use the following command (NOTE: This should be run outside of the build/ directory i.e. cd ../)

./bin/Transform_4OPH

• This will output a CHARMM formatted PSF and coordinate file for visualizing the unit crystal
• This will also output two PDB coordinate files for the unit cell and the super cell in the data/ directory

3.) Create a CHARMM PSF and coordinate file for the unit and super cells

• This step is only if you need a CHARMM PSF and coordinate file

cd data/
charmm < build_4oph_unit.inp > out_build_4oph_unit.out
charmm < build_4oph_super.inp > out_build_4oph_super.out

4.) View the unit cell and super cell in VMD

vmd -e view_4oph_unit.vmd
vmd -e view_4oph_super.vmd

Generate Coordinates for Unit Cell, Super Cell and Perform Arbitrary

Transformations 0.) Configure

• Adjust the output file names in the driver file

1.) Compile

./compile.sh

OR

mkdir build
cd build/
cmake ..
make -j

2.) Run the code

• For this example you can use the following command (NOTE: This should be run outside of the build/ directory i.e. cd ../)

./bin/Transform_2Y2A

• This will output a CHARMM formatted PSF and coordinate file for visualizing the unit crystal
• This will also output three PDB coordinate files for the unit cell and the super cell in the data/ directory

3.) Create a CHARMM PSF and coordinate file for the unit and super cells and stacked unit cell

• This step is only if you need a CHARMM PSF and coordinate file

cd data/
charmm < build_2y2a_unit.inp > out_build_2y2a_unit.out
charmm < build_2y2a_super.inp > out_build_2y2a_super.out
charmm < build_2y2a_stack.inp > out_build_2y2a_stack.out

4.) View the unit cell and super cell in VMD

vmd -e view_2y2a_unit.vmd
vmd -e view_2y2a_super.vmd
vmd -e view_2y2a_stack.vmd