Run AlphaFold in ChimeraX for cryoEM model building 

AlphaFold works on a single protein sequence. I have heard people try to put a linker between two proteins to make it a single sequence and then run AlphaFold with mixed results. I would not expect that to work well because the multiple sequence alignment AlphaFold produces to predict the long range contacts won't include sequences spanning the linker so I would not think it would provide any info about inter-protein contacts. Also AlphaFold crashes on longer sequences running out of GPU memory. The EBI AlphaFold database limited sequences to 1400 amino acids and that used the memory from 4 GPUs. The ChimeraX AlphaFold prediction can only use one GPU and seems limited to about 800 amino acids.