Converting AlphaFold3 CIF to PDB: Difference between revisions
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If your .cif file had 5-character ligand codes (instead of or in addition to 3-character ligand codes), conversion will truncate those 5-character codes to their first three characters. | If your .cif file had 5-character ligand codes (instead of or in addition to 3-character ligand codes), conversion will truncate those 5-character codes to their first three characters. | ||
(5-character ligand names were introduced after all 3-character codes were in use.) | (5-character ligand names were introduced after all 3-character codes were in use.) | ||
For example, the ligand code A1EJM in [[9l63|9L63]] will be truncated to A1E in the converted PDB file. FirstGlance will handle it correctly except that under ''Ligands and Non-Standard Residues'' (in the Molecule Information Tab), '''the link (=?) will display the wrong chemical structure'''; namely, it will display ligand A1E instead of A1EJM. | For example, the ligand code [https://www.rcsb.org/ligand/A1EJM A1EJM] in [[9l63|9L63]] will be truncated to A1E in the converted PDB file. FirstGlance will handle it correctly except that under ''Ligands and Non-Standard Residues'' (in the Molecule Information Tab), '''the link (=?) will display the wrong chemical structure'''; namely, it will display ligand A1E instead of A1EJM. | ||
To display the chemical structure of a ligand with a 5-character code, go to [http://rcsb.org RCSB.org] and enter the 5-character code into the search slot at the top, then press Enter. | To display the chemical structure of a ligand with a 5-character code, go to [http://rcsb.org RCSB.org] and enter the 5-character code into the search slot at the top, then press Enter. | ||
