Hi Theo, quick answer: you need CCmask for your purpose[*] and I don't know exactly what version of CC LigandFit computes and reports. Longer answer: for this kind of benchmarking, it is essential to use the exact same definition of CC and the exact same code (with identical settings) to compute it. If you are comfortable with Python scripting and familiar with CCTBX, I can send you a script that demonstrates how to do this. Pavel [*] https://journals.iucr.org/d/issues/2018/09/00/kw5139/index.html On 7/29/25 11:34, Theo Teng wrote:
Dear Phenix developers,
I hope this message finds you well.
We had two specific questions about how the real-space correlation coefficient (RSCC) is computed when using Phenix.LigandFit:
1. What radius is used around the ligand or search center when calculating the RSCC during ligand fitting? Is this radius fixed or adaptive?
2. Which CCTBX function(s) underlie the RSCC calculation used in LigandFit?
We aim to compare the placements from LigandFit to other ligand placement methods, and your response would be appreciated.
Best regards,