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]] 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 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. | ||
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To list all the ligand codes in your .cif file, after dropping the .cif file into the black window of Jmol.jar, enter these two '''bold commands''' in the white window: | To list all the ligand codes in your .cif file, after dropping the .cif file into the black window of Jmol.jar, enter these two '''bold commands''' in the white window: | ||
< | For example 9dos: | ||
<br> | |||
<span style="color:magenta;">$</span> '''select ligands''' | <span style="color:magenta;">$</span> '''select ligands''' | ||
</ | <br> | ||
94 atoms selected | |||
<br> | |||
<span style="color:magenta;">$</span> '''show residues''' | |||
<br> | |||
<span style="color:blue;">[GOL]501:A | |||
<br> | |||
[A1A8V]502:A | |||
<br> | |||
[A1A8V]501:B | |||
<br> | |||
[A1A8V]501:C | |||
<br> | |||
[A1A8V]501:D</span> | |||
GOL is a 3-character ligand code (for glycerol), and A1A8V is a 5-character ligand code. "501:D" means residue number 501 in chain D. | |||
==See Also== | ==See Also== | ||
