Converting AlphaFold3 CIF to PDB: Difference between revisions
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<li> [http://firstglance.jmol.org/where.htm#uploading Upload] ''jobname.pdb'' to [http://firstglance.jmol.org FirstGlance in Jmol]. | <li> [http://firstglance.jmol.org/where.htm#uploading Upload] ''jobname.pdb'' to [http://firstglance.jmol.org FirstGlance in Jmol]. | ||
</ol> | </ol> | ||
===Caution: Ligand Names May Be Wrong=== | |||
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.) | |||
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. | |||
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 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: | |||
<pre> | |||
<span style="color:magenta;">$</span> '''select ligands''' | |||
</pre> | |||
==See Also== | ==See Also== | ||
