ASL to get proteic structure

[Sebastian Contreras]

Hi

I have a question. how can i do the ASL to select only the protein. for example in my case I need to get the proteic structure of every frame of a MD and I have programmed this

    csim = DesmondSimulation('MD-out.cms', 'MD_trj')
    total=csim.total_frame
    for i in range (total):
        frame = csim.getFrame(i)
        st = frame.getStructure()
        name="frame_"+str(i)+".mae"
        st.write(name)

but it save me waters, ions and the protein

best

Sebastian

[Dave Giesen]

Hi Sebastian - we have a 'protein' alias in our ASL language that does what you want. I would modify your code as follows to write only the protein structure:

from schrodinger.structutils import analyze  ### New line

csim = DesmondSimulation('MD-out.cms', 'MD_trj')
total=csim.total_frame
for i in range (total):
    frame = csim.getFrame(i)
    st = frame.getStructure()
    name="frame_"+str(i)+".mae"

    protein_atoms = analyze.evaluate_asl(st, 'protein')  ### New line

    protein = st.extract(protein_atoms, copy_props=True)   ### New line
    protein.write(name)   ### Modified line

The 'protein' alias selects all atoms that are either part of a residue that has a Calpha carbon or are part of an ACE residue.

Dave

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