[ccp4bb] Questions about PanDDA modelling and refining

2024-07-29 Thread Vladyslav Yadrykhinsky
Hello, I am learning how to use PanDDA and would appreciate some clarifications on the modeling and refining steps. I realize that maybe some questions will be too obvious, but I would appreciate the confirmation of my guesses so I might learn to do it the correct way. I managed to get to step

[ccp4bb] ZipperDB database access issue

2024-07-29 Thread Das, Abhinaba
Dear Community, There is this nice web server, ZipperDB (https://services.mbi.ucla.edu/zipperdb/intro), that predicts the fibrillogenic propensity of a given peptide segment. However, it seems to have been down for a couple of months now. I have emailed them a few times but have not received a

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

2024-07-29 Thread Javier Gonzalez
Thank you all for your thoughtful answers. I'll stick to the crystallographic data and model as much as I can with reasonable occupancy and B factors, even if the result is a truncated model. I don't believe in the zero occupancy trick either. I just thought the PDB was more flexible these days,

[ccp4bb] Biological Cryo-EM Expert Position - UC Irvine

2024-07-29 Thread Celia Goulding
Dear All The University of California, Irvine is currently accepting applications for a specialist position to manage the day-to-day operations of the biological side of the electron microscopy facilities and services to users at the UC Irvine Materials Research Institute (IMRI) see https://im