Dear Ansuman, The PDB_REDO server has extensive ligand validation, but it won't tell you explicitly whether the ligand is there or not. You have to figure that out from the validation scores. High real-space R values or low real-space correlation coefficients are a hint that your ligand isn't there. High energy of formation indicates ligand strain which may also be the result of building a ligand that is either non-existent or just misidentified. Poor ligand-binding site interactions are also informative, but are sensitive to the chemical properties of the ligand.
Cheers, Robbie Sent from my Windows Phone ________________________________ Van: ansuman biswas Verzonden: 20-9-2014 0:08 Aan: [email protected] Onderwerp: [ccp4bb] software or server to validate ligand density Dear All, I have collected a diffraction dataset from a crystal soaked in a solution containing the ligand of interest. After refining a few cycles, I can see some density in the active site pocket, but not so clear to model the ligand unambiguously. Is any tool available to validate whether the ligand is actually there or not ? The Twilight server appears to be for PDB files that have already been deposited. thanks and regards, Ansuman Biswas, dept. of Physics, Indian Institute of science
