Hi Benedikt,
You can do a work around with '<' or '>':
Sele qm, q>0.9999999 and q<1.0000001
I checked that this works like this for my "obj" in PyMOL:
stored.q = []
iterate obj, stored.q.append(q)
q_arr = np.array(stored.q)
q_1 = q_arr[q_arr == 1] # only keep values of q that equal 1
print(len(q_1))
You can make actually use this numpy feature to slice the atom indices into an
array (lets say atom_arr) then make a selection with it like this:
cmd.select("qm",f"index {'+',join(atom_arr)}")
But '<' or '>' operators are quicker and seem safe
Kind regards,
Ali Kusay
Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
On 12/2/21, 11:34 pm, "Benedikt Floeser" <[email protected]> wrote:
Dear fellow users,
among other things I use pymol to edit PDB files so as to use them in
an ORCA calculation. This entails changing the occupancy and B-factors
to values of 0, 1 and 2.
Changing these entries to the appropriate values but selecting, e.g.,
all atoms with a q value of 1 or 1.00 with something like
'select qm, q = 1' fails whereas it works with partial charges or
formal charges. Is there any way to do this without resorting to
workarounds with '<' or '>'?
Best
--
Dr. Benedikt M. Flöser
Max-Planck-Institute for Chemical Energy Conversion
Stiftstraße 34-36
45470 Mülheim a.d. Ruhr
Germany
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