RecursiveRMScheck calculates Root Mean Square Devation (RMSD) between all pdb pairs in the recursive folders one by one and generates RMSD file of each folder into outputs folder.
To use this tool, you should have two input directories with the names of pdbfolders and scripts.
- pdbfolders folder includes the subdirectories with the name of mutations and each folder contains the generated 6 models. You need to generate list_foldernames.txt which includes the folder names.
- scripts folder contains two script files:
- rmsd.pml is the PyMOL script that calculates the RMSD between two given pdb files. So, it is important to note that to be able to use this script you should have PyMOL downloaded in your computer. If not you can dowload from the link.
- RMSD_calculation.csh uses rmsd.pml script to generates RMSD files as RMS__foldername_ into the outputs folder.
When you are in the scripts directory, use below command to run the script.
$ ./RMSD_calculation.csh
outputs folder contains the final RMS files of each folder.
Note1: RMSD calculation is performed by using PyMOL. So, if you do not have it on your computer, you can dowload from the link.
Note2: Please do not forget to change the path of PyMOL with the correct path in your computer!
If you have any questions, please contact with burcu.ozden@ibg.edu.tr