Hi everyone,
I would like to ask how to export the lists from geometry restrains of MolProbity after running Phenix real-space refinement.
I have tried to read real_space_refine_xx.pkl under .phenix/project_data through phenix.python. Here I could find some information about bonds, angles, and so on. But I could not decode the result( Please see below). I guess each element(like [122488, 122490]) represents one pair of atoms. But how could I decode the atom information, ideal value, model value, and deviation based on this number?
I am looking forward to the solution. Many thanks in advance!
Best,
Shaocheng.
pkldata.validation_cryoem.model.geometry.bond
group_args
max : 0.578805129498
mean : 0.00880050872911
min : 3.41948691585e-14
n : 148592
outliers : [[122488, 122490], [45765, 45767], [133694, 133696], [56971, 56973], [56972, 56973], [133695, 133696], [122489, 122490], [45766, 45767], [9567, 9569], [86290, 86292], [122485, 122487], [45762, 45764], [1867, 1869], [78590, 78592], [133691, 133693], [56968, 56970], [78590, 78591], [1867, 1868], [122485, 122486], [45762, 45763], [133691, 133692], [56968, 56969], [78593, 78595], [1870, 1872], [1871, 1872], [78594, 78595], [87231, 87232], [10508, 10509], [45763, 45765], [122486, 122488], [86251, 86252], [9528, 9529], [85348, 85350], [8625, 8627], [86251, 86253], [9528, 9530], [139333, 139335], [71476, 71478], [87045, 87046], [10322, 10323], [133692, 133694], [56969, 56971], [35410, 35420], [56970, 56972], [133693, 133695], [12379, 12381], [87045, 87047], [10322, 10324], [89102, 89104], [89103, 89104], [12380, 12381], [86254, 86256], [9531, 9533], [45764, 45766]
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