No atom within a given radius.

[sharma1420]

May you please help me,

I have a PDB format of crystal structure file( LiV3(TeO6)2. I want to find the no of atoms around each Li within a 4 A radius in the unit cell. I try to replicate the same as following,

st = gemmi.read_structure('/Users/rahul/Downloads/structure.pdb')
ns = gemmi.NeighborSearch(st[0],st.cell,4).populate(include_h=False)
ref_atom = st[0].sole_residue('',gemmi.SeqId('1')).sole_atom('Li')
marks = ns.find_neighbors('Li',min_dist=0.1,max_dist=4)
len(marks)

[wojdyr]

Did you get an error?
Note that in your script the first argument to find_neighbors is 'Li' instead of ref_atom.

[sharma1420]

May you please guide me on exactly what I am doing wrong here?

I attached the error and Crystal structure file screenshot.

[wojdyr]

In your previous screenshot you got the residue correctly (the chain name is empty in your PDB file), but the atom was not found because the name comparison is case sensitive (in the file it's LI not Li).

[sharma1420]

Oh, yes, sir, I got it.

Thank you.

[sharma1420]

sorry to bother you again,

in another search,
I got an error of Run time error: Multiple alternative atom LI.

[wojdyr]

It means that you have multiple atom sites with the same name (alternative conformations).
sole_atom('LI') checks if there is only one such atom. You can use find_atom() instead.