PDB keywords to define active sites, extra ligands etc.

What keywords are required in a PDB file to be able to use 'zoom to pocket' and 'select neighbourhood' commands?





In other words, if I output a PDB file from a modelling package then quite often the keywords such as SITE etc aren't defined or included. How do I get MSpace to recognise ligands, active sites etc.?





Thanks,


Mike

Hi Mike,





one HETATM block (that is, several HATATM records) is the minimum. MarvinSpace's PDB import module also recognizes the COMPND, HET and HATNAM records which are also related to ligands.


The SITE keyword, however, is not yet processed. If you need that, please let us know and we implement it.





If your structure is not a complex and only the macromolecule is defined but not the substrate then the 'zoom to pocket' function is not available. If this is the case, please tell us what would be the most convenient solution for you and we implement it.





Regards,


Miklos