Structure prediction

Training

amo semer3d \
-train \
-dirt training_data/ \
-index training_data/index_list \
-mbs 128 \
-echo 20000 \
-threads 8
# Checkpoint
# -param /path_to_pre_trained_model/XXXXX.pt

Prediction

amo semer3d \
-param /path_to_pre_trained_model/XXXXX.pt \
-n MAXIMUM_LENGTH \
-fastx XXXXX.fasta

Assembly

#!/bin/bash

pdb_lst=pdblst
pml=pymol_pml.pml

n_fragment=16

echo "delete all" > ${pml}
for i in `seq 1 ${n_fragment}`
do
  pdb_1=`head -${i} ${pdb_lst} | tail -1`
  echo "load ${pdb_1}, AmoAi_${i}" >> ${pml}
done
n_fragment=`expr 16 - 1`
for i in `seq 1 ${n_fragment}`
do
  k=`expr ${i} + 1`
  echo "align AmoAi_${k}, AmoAi_${i}" >> ${pml}
done
echo "save AmoAi_tmp.pdb, state=-1" >> ${pml}
pymol -c ${pml} > /dev/null

${amo} pdb_trim \
-jobname pdb_assembly \
-kind pdb \
-pdb AmoAi_tmp.pdb \
-type 1 \
-offset 1200 \
-chain A \
-re 1 \
-n 1

Case study

The Vps13 contains 3144 amino acids. (Vps13, YLL040C, Yeast)

More examples can be found at this link.