On 03/11/2023 20:57, Ma, Boyuan wrote:
Dear Cooters,
I want to use a python script to select several disconnected fragments
to perform refinement in one time, for example,
"coot.some_refinement_by_residue_range(imol, /1/A/1-20 || /1/A/22-30)."
However, after searching previous messages in the mail list, I still
do not know what the right format is for selecting these fragments in
one string.
BTW, thanks for Joel's answers.
https://www.mail-archive.com/coot@jiscmail.ac.uk/msg01933.html. It
does help me a lot.
"atom_selection_string is the 'standard' mmdb atom selection string,
explained in detail in the *mmdb manual*."
And the mmdb manual can be seen at here:
https://www.ccp4.ac.uk/html/pdbcur.html#atom_selection
<https://www.ccp4.ac.uk/html/pdbcur.html#atom_selection>
Crikey - that was a while ago (hello Joel).
I presume that you are using Coot 0.9x.
There is a "new" API interface to the real space refinement now:
refine_residues() which takes a list of residue specs
def make_res_range(start_res_no, end_res_no):
l = range(start_res_no, end_res_no + 1)
r = [["A", i, ""] for i in l]
return r
range_1 = make_res_range(10, 20)
range_2 = make_res_range(30, 40)
combi_range = range_1 + range_2
imol = read_pdb("tutorial-modern.pdb")
imol_map = read_mtz("rnasa-1.8-all_refmac1.mtz", "FWT", "PHWT", "", 0, 0)
refine_residues(imol, combi_range)
(Needless to say, this is different in the new version).
Regards,
Paul.
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