BSI wiki

ssh jmwadmin@pollux

bash

conda activate model_angelo

This is the recommended use case, when you have access to a medium-high resolution cryo-EM map (resolutions exceeding 4 Å) as well as a FASTA file with all of your protein sequences.

Let's say the map's name is map.mrc and the sequence file is sequence.fasta. To build your model in a directory named output, you run:

model_angelo build -v map.mrc -f sequence.fasta -o output

If the output of the program halts before the completion of GNN model refinement, round 3 / 3, there was a bug that you can see in output/model_angelo.log. Otherwise, you can find your model in output/output.cif. The name of the mmCIF file is based on the output folder name, so if you specify, for example, -o testing/test/model_building, the model will be in testing/test/model_building/model_building.cif.

If you have a sample where you do not know all of the protein sequences that occur in the map, you can run model_angelo build_no_seq instead. This version of the program uses a network that was not trained with input sequences, nor does it do post-processing on the built map.

Instead, in addition to a built model, it provides you with HMM profile files that you can use to search a database such as UniRef with HHblits.

You run this command:

model_angelo build_no_seq -v map.mrc -o output

The model will be in output/output.cif as before. Now there are also HMM profiles for each chain in HHsearch's format here: output/hmm_profiles. To do a sequence search for chain A (for example), you should first install HHblits and download one of the databases. Then, you can run

hhblits -i output/hmm_profiles/A.hhm -d PATH_TO_DB -o A.hhr -oa3m A.a3m -M first

You will have your result as a multiple sequence alignment here: A.a3m.