Hi all, Im wondering about occupancy refinements - both what's going on under the hood and what are best practices.
In the example I have, there is a ligand found in two distinct, partially overlapping sites that can be modeled is some confidence, but likely there are very low occupancy additional poses that blurs the electron density. The modeled poses are known from prior work, so even though there is smearing we know the ligand is in the modeled conformation. After perturbing the crystal these I am trying to decide what the best approach is to get some sort of numerical occupancy value to describe the distribution. 1. In Phenix, how is the occupancy number determined? Is there a real-space correlation between the experimental density and the model(weighted to occ) that is optimized? How can this go wrong? I fear that the smearing and heterogenous nature will through the refinement off (over or underfitting to periphery density rather than hyper-localized position of the model) 2. Are there errors associated with the occupancy numbers? 3. For my own testing, I did 5% increments and manually observed Fo-Fc and 2Fo-Fc maps and selected a value that resulted in the lowest amount of both positive and negative Fo-Fc peaks. This is how we submitted the work to journal but reviewer wants it to be automatically calculated. Is my approacg problematic besides the subjective nature of me determining what is a minimized peaks? Is this less so reliable to automated fitting? Will this really make a difference? To be most honest, how should I let phenix approximate these values? Set B-factor to average protein b? Refine both simultaneously? Or? Any insight would be appreciated. Matt ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
