Open FilomenoSanchez opened 7 months ago
5a3h_sigmaa.mtz
doesn't contain an R-free column hence the function is working as expected - no recalculation of the map and no differences in the difference map.
Capture the return value of sfcalc_genmaps_using_bulk_solvent()
and test for r_factor
= -1. That will tell you that the structure factor calculation failed.
I will let you close this.
Hi @pemsley, the return value of sfcalc_genmaps_using_bulk_solvent
seems to suggest there's nothing wrong with the structure factor calculation (at least as far as I can tell based on the r_factor
field):
{
r_factor: 0.10371405631303787,
free_r_factor: 0.15522709488868713,
bulk_solvent_volume: 0.25201278924942017,
bulk_correction: 0.2925781309604645,
n_splines: 16
}
Also 5a3h_sigmaa.mtz
does have a Rfree column (albeit mtzdmp prints weird asterisks that I haven't seen before):
$ mtzdmp ./5a3h_sigmaa.mtz
[ ... ]
Col Sort Min Max Num % Mean Mean Resolution Type Column
num order Missing complete abs. Low High label
1 ASC 0 30 0 100.00 11.2 11.2 14.90 1.82 H H
2 NONE 0 38 0 100.00 14.4 14.4 14.90 1.82 H K
3 NONE 0 42 0 100.00 15.7 15.7 14.90 1.82 H L
4 NONE 0.********* 0 100.00****************** 14.90 1.82 I FREE
5 NONE 11.9 1539.1 0 100.00 184.69 184.69 14.90 1.82 F FP
6 NONE 2.1 68.9 0 100.00 12.83 12.83 14.90 1.82 Q SIGFP
7 NONE 0.1 2864.1 0 100.00 206.89 206.89 14.90 1.82 F FC
8 NONE 0.0 360.0 0 100.00 176.87 176.87 14.90 1.82 P PHIC
9 NONE 0.0 1451.5 0 100.00 173.86 173.86 14.90 1.82 F FC_ALL
10 NONE 0.0 360.0 0 100.00 178.31 178.31 14.90 1.82 P PHIC_ALL
11 NONE 0.0 1626.7 0 100.00 176.99 176.99 14.90 1.82 F FWT
12 NONE 0.0 360.0 0 100.00 178.33 178.33 14.90 1.82 P PHWT
13 NONE 0.0 858.1 0 100.00 54.44 54.44 14.90 1.82 F DELFWT
14 NONE 0.0 360.0 0 100.00 178.24 178.24 14.90 1.82 P PHDELWT
15 NONE 0.001 1.000 0 100.00 0.882 0.882 14.90 1.82 W FOM
16 NONE 0.1 2062.3 0 100.00 203.85 203.85 14.90 1.82 F FC_ALL_LS
17 NONE 0.0 360.0 0 100.00 178.38 178.38 14.90 1.82 P PHIC_ALL_LS
And finally, if instead of 5a3h.pdb
and 5a3h_sigmaa.mtz
I use moorhen-tutorial-structure-number-1.pdb
and moorhen-tutorial-map-number-1.mtz
I still see the same behaviour (test does not pass).
I have a different version of 5a3h_sigmaa.mtz
to you, it seems.
OK.
We seem to be getting an empty vector back from
molecules_container::get_diff_diff_map_peaks
. Here's the test that is currently failing: