I am trying to follow a workflow example of how to do a pharmacophore. I have the PDB with the structure of my protein and my molecule in my laptop (it comes from a Cryo-EM). I have used several different ways (as appear in the picture or with load local pdb files node) with to firstly obtain fragment information.
I am able to see the protein and generate the sequence of my protein but when I try to do the fragment, it is impossible. The following error appears, when I have tried by different ways.
ERROR Fragment information 4:1 Execute failed: jp.co.infocom.cheminfo.marvin.type.MrvBlobCell cannot be cast to org.knime.core.data.def.StringCell
WARN PDB Sequence Extractor 4:13 No PDB column selected.
WARN Fragment information 4:14 Column ‘pdb_code’ automatically chosen as identifier column
ERROR Fragment information 4:14 Execute failed: BAD REQUEST
I would really appreciate it if someone could help me, please.
Thank you very much