Exercise III - Fingerprints

1. Exercise III - Fingerprints • Open SSH Secure Shell Client, and log in the host gaviaowith the user name guest0? (password smscg). • Type $cd FINGERPRINT to enter in the directory. • Type $ pico Input to edit the FINGERPRINT input file. • Select (typing) “LIG” (to calculate the surface of the ligand) or “CAV” (to calculate the cavity surface). This choice must be written in line 27. To see line numbers, type “Ctrl C”. When ready, type “Ctrl X” to exit, “Y” to confirm and “Enter” to overwrite in the same file. • Type $ ll PDB/ to check if the directory PDB contains the file to calculate the fingerprint. In case it doesn’t, type $ cp /pdb/filename.pdb ./PDB • After that, type $ pico pdb_list and write “ filename.pdb” . • When everything is ready, type $ fingerprint to run the algorithm. • If you selected LIG, type $ mv PDB/filename.kin PDB/filename_lig.kin • If you selected CAV, type $ mv PDB/filename.kin PDB/filename_cav.kin • Now, do the same selecting LIG if you’ve done the CAV, or selecting CAV if you’ve done the LIG. http://www.cbi.cnpia.embrapa.br

2. Visualizing the fingerprints • To see the contour maps generated in the program FINGERPRINT, type • $ cd PDB. • Now, type “mage”. • A graphic window will open in your display (if doesn’t call us!). • Click in the “Proceed” icon. • Click “File”, “Open New Kin File”. • Select your filename.kin and click “OK”. http://www.cbi.cnpia.embrapa.br