Folks:
I have tried to contact the BIOVIA DiscoveryStudio support team, somehow my browser does not allow me to open their "contact form". I am trying to visualize and perform an analysis on a protein:smaller molecule complex. The smaller molecule happens to be a long peptide. Whatever I do with the PDB (change ATOM cards to HETATM, change residue names to PEP, UNK, LGD, introduce MODEL and ENDMDL cards) DiscoveryStudio indicates the input PDB file doesn't contain any ligand. Would any on ResearchGate have an idea of how to specify that a part of a coordinate file is the ligand, so that DiscoveryStudio 2021 recognises it as such and allows me to proceed? Thanks, Fred.
You can use Ctrl+H to get the hierarchy table and from there you can manually locate the part of the pdb where your ligand is present then after selecting the ligand from the hierarchy table, you can click on Define Ligand in the tools menu present in left side of program. You can access the tools menu if it is not present by going to "View" drop-down , "Explorer" and then selecting tools. Hope that helps.
Frederic Vellieux , after defining the receptor and ligand molecule in the analysis and clicking on ligand interactions, you can see the option in middle bottom the program which will open a dialog box (Data Table) upwards, you can also use the shortcut Ctrl+T (screenshot attached) then you can click on "non-bond" to get the table for the information about the interactions (screenshot # 2). Hope this helps.
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