Hi Harry,
As a so so crystallographer (7 years in the field) I do exactly what Randy
said we should not. If running a single molecule I just download the model from
the AF database. If it is a complex I prepare the model using the AF server. If
MR works, then it is the time to fix things. I remove everything that has no
electron density in the map and also trim some loops and disordered regions
that make no sense. If my model is not complete, then I slowly add Ala to the
gaps and refine it to check if I can see any electron density showing up. If
yes, I mutate it to the right amino acid and refine my model again, but if no I
just stop buidling my sequence. I keep doing this until barely nothing changes
after refinement. After adding water and fitting some of the blobs, if the
stats are good and around the expected for a model at a certain resolution,
it`s time for deposition.
Best wishes
______________________________________________________
Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester
Mestre em Física Biomolecular
Universidade de São Paulo
Bacharel em Ciências Biológicas
Universidade Federal de São Carlos
phone: +44 07861 273773
"A sorte acompanha uma mente bem treinada"
________________________________________________
________________________________
De: CCP4 bulletin board <[email protected]> em nome de Harry Powell
<[email protected]>
Enviado: sábado, 24 de janeiro de 2026 15:56
Para: [email protected] <[email protected]>
Assunto: [ccp4bb] pruning & confidence of AlphaFold models for MR
Hi folks
I’m sure that people have thought about this, done this, and maybe even
published on the topic, so this should be an easy one to answer :-)
I was wondering how people treat AlphaFold models when using them in molecular
replacement? Do they prune them down to poly Ala, do they include all modelled
residues or remove those with low confidence (if so, how low - pLDDT 70?)?
Harry
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