Opened 4 years ago

#6618 assigned enhancement

Allow alphafold fetch or predict for a specified PDB identifier

Reported by: phil.cruz@… Owned by: Tom Goddard
Priority: moderate Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

Phil says a user asked during his alphafold pae presentation about fetching alphafold models using PDB identifier.

This could be added. Usually the purpose of this is to compare the PDB structure and the AlphaFold model. Currently you can open the PDB model (e.g. open 7whw) and then the AlphaFold tool will list the model and its chains for fetching and predicting, for instance #1/A, #1/B, #1. Specifying the model without a chain means fetch or predict for all chains.

The alphafold match and predict commands also accept open PDB model and chain specifiers (e.g. alphafold match #1)

So I am not sure directly specifying a PDB identifier is a useful case. An advantage of opening the PDB first is that the fetched or predicted AlphaFold models will automatically be aligned to the PDB model using matchmaker.

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