Running FATCAT 1.0 (Ye and Godzik, 2003) will allow users to run the flexible protein alignment tool needed to run some of the methods Recommended to verify that FATCAT is running properly prior to running methods such as ‘ImportGlob’
Materials Download the folder ‘protein comparison tool’ from Github
Before Beginning Have Anaconda & JAVA installed Anaconda: https://docs.anaconda.com/anaconda/install/windows/ JAVA: https://www.java.com/en/download/ (For Windows OS) have WSL installed (WSL installation manual) https://docs.microsoft.com/en-us/windows/wsl/install-manual#step-3---enable-virtual-machine-feature
Running FATCAT in the command prompt enter: bash runFATCAT.sh -pdb1 pdbID(enter pdb id here) -pdb2 pdbID(enter 2nd pdbID here) -pdbFilePath /(enter path to pdb files here)/ -autoFetch -printFatCat -flexible
Ex: bash runFATCAT.sh -pdb1 1ake -pdb2 2ake -pdbFilePath /Users/name/Documents/pdb_file_folder/ -autoFetch -printFatCat -flexible
Clone the Protein Comparison Tool repository
Install the latest version of Java: https://www.java.com/en/download/ Install Pymol: https://pymol.org/2/
Make sure the following libraries are installed: requests BeautifulSoup pandas
*Enter pdbDirectory and outputDirectory as prompted
getHomologData(genename, targetprotein, pdbidlist)
Returns a dataframe and excel spreadsheet ("genenamedata.xlsx") including pdb id, uniprot id, organism, pdb entry name, global stoichiometry, length, associated pubmed ID(s), and Taxonomy for each pdb in pdbidlist
importGlob(pdb1, pdb2) Runs FATCAT and saves alignment as a cif file
ChainByChain(pdb1,pdb2) Runs FATCAT between every chain in both PDB inputs and returns cif file for every alignment
fatcat_savexml(pdb1,pdb2) Runs FATCAT and saves alignment as an xml file