[phenixbb] Problem with rebuild_predicted_model

[Andrei Moiseenko]

Dear all,

 

I am trying to build the model with Alphafold2 using Dock and Rebuild and
encountered some issue with rebuild_predicted_model. It does not rebuild the
model telling that: "Unable to morph model...may not match exactly in chain
ID or residue numbers. No morphed model obtained... No docked model to work
with."

I use the model predicted with Alphafold2 google colab and the cryoem map
with 3.5A resolution boxed around the protein of interest. The
process_predicted_model and dock_predicted_model run successfully, giving
the single-chain model which nicely fits into the map (40 of 300 residues
are excluded due to low LDDT). The chain ID in the docked model is indeed
different from predicted model: the predicted model has one chain A, but the
docked one has A1. However, manually changing the chain ID either in the
predicted or in the docked model does not resolve the issue. Manual runs of
rebuild_predicted_model also fail with the same result.

Tried it with models and maps for different proteins, tried both on Linux
and Windows - it gives the same output (Phenix 1.20.1.-4487). Please, find
the log attached. I am seeking for any advice on resolving this problem. 

 

 

Best regards
Andrey Moiseenko

Electron Microscopy Lab @ Biology Department
Moscow State University
 <mailto:postmoiseenko at gmail.com> postmoiseenko at gmail.com 
skype: callmoiseenko

 

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