I have used this web site to generate SMILES strings from PDB coordinates. You need to strictly examine the output to ensure that you get the proper chirality, bond order and correct number of hydrogens, and if there are discrepancies you may have to edit the string.
Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) On Sep 13, 2024, at 10:28 AM, Hekstra, Doeke Romke <doeke_heks...@harvard.edu> wrote: EXTERNAL MAIL Hi, Does anyone have experience (or scripts!) to extract ligand SMILES from macromolecular PDB records using the PDB data API or from a library of PDB or mmCIF files? We would greatly appreciate any pointers to get us started. Thank you, Doeke ===== Doeke Hekstra Assistant Professor of Molecular & Cellular Biology, and of Applied Physics (SEAS), Director of Undergraduate Studies, Chemical and Physical Biology Center for Systems Biology, Harvard University 52 Oxford Street, NW311 Cambridge, MA 02138 Office: 617-496-4740 Admin: 617-495-5651 (Lin Song) ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!MznTZTSvDXGV0Co!GPbhXSnaWPxjCLmQuuy9EfcXLQsBXcNcyCuHjqJhfqOoNq9ubSUeD9W3yhtZhQ4PtLlYEhJrEOW__WP78mYhm7jtHym8xLQtPMk_omJS$> CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. ________________________________ UT Southwestern Medical Center The future of medicine, today. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
