Hi all
It seems that adding ncs ghosts and then ncs maps is broken for my
model / coot combo.
Coot is at ver 0.6-pre-1 rev 2334.
Thanks!
This is what phenix.simple_ncs_from_pdb gives me
==================== Process input NCS or/and find new NCS
====================
NCS groups found in parameter file: 1
NCS group 0:
reference= chain A and (resseq 1:39 or resseq 43:54 )
selection= chain B and (resseq 1:39 or resseq 43:54 )
Automatic NCS search:
# simple_ncs_from_pdb
#
# Find ncs among chains in a PDB file
# type phenix.doc for help
Getting NCS from suggested chains:
RMSD for suggested group ['A', 'B'] [[[1, 39], [43, 54]], [[1, 39],
[43, 54]]] is 0.0121907468281
Updated/new NCS groups:
refinement.ncs.restraint_group {
reference = chain 'A' and (resseq 1:39 or resseq 43:54 )
selection = chain 'B' and (resseq 1:39 or resseq 43:54 )
}
----------Building NCS restraints----------
NCS restraint group 1:
NCS operator 1:
Reference selection: "chain A and (resseq 1:39 or resseq 43:54 )"
Other selection: "chain B and (resseq 1:39 or resseq 43:54 )"
Number of atom pairs: 1103
Rotation={{-0.500763, -0.865584, 0.000393409},
{-0.865584, 0.500763, 0.000526561},
{-0.000652788, -7.68463*^-05, -1}}
Translation={{-53.5412}, {-30.8968}, {104.68}}
Histogram of differences:
0.000454 - 0.008521: 479
0.008521 - 0.016588: 422
0.016588 - 0.024655: 146
0.024655 - 0.032722: 40
0.032722 - 0.040790: 13
0.040790 - 0.048857: 3
RMS difference with respect to the reference: 0.013137
However when I try to overlay ncs ghosts and a ncs map I get this from
coot
NCS_controller display chain toggled for imol 0 chain 1 state 1
%%%% ncs_control_display_chain
There are 1 ghosts
ighost: 0
name: "NCS found from matching Chain B onto Chain A"
chainid: B
target chain id: A
display_it_flag 1
%%%%%%%%% calling fill_ghost_info() from c-interface.cc
make_ncs_ghosts_maybe()
INFO:: NCS chain comparison 51/51
First atom of 1103 in first selection 1/A/1/Gr/ P altLoc ::
segid :A: pos: (-26.744,-11.257,24.195) B-factor: 106.43
First atom of 1103 in second selection 1/B/1/Gr/ P altLoc ::
segid :A: pos: (-30.371,-13.357,80.514) B-factor: 107.38
WARNING - no residue for reference residue number 40 A
WARNING - no residue for moving molecule residue number 40 B
WARNING - no residue for reference residue number 41 A
WARNING - no residue for moving molecule residue number 41 B
WARNING - no residue for reference residue number 42 A
WARNING - no residue for moving molecule residue number 42 B
WARNING:: no points to do matching
find_ncs_matrix returns (LSQ) junk
| 0, 0, 0|
| 0, 0, 0|
| 0, 0, 0|
( 0, 0, 0)
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
INFO:: installing ghost map with name :NCS found from matching Chain B
onto Chain A
Done install_ghost_map
Reference matcher: 0 and 0
|6.953e-310,6.953e-310,6.953e-310|
|2.238e-314, 1.16e-315,1.334e-322|
|4.244e-314,4.032e-321, 0|
(2.144e-314, 0, 0)
inverse of reference matcher transformation:
| nan, nan, nan|
| nan, nan, nan|
| nan, nan, nan|
( nan, nan, nan)
boxing over uvw = ( -0.6365, -0.3535, 0.08703) to uvw =
( 0.2349, 0.1764, 0.6158)
INFO:: There were 2 maps contributing to the average
INFO:: rescaling by 0.5
INFO:: 316520 out of 331872 (95.3741%) map points were masked out of
NCS average target volume, chain A
INFO:: made 1 averaged map(s)
Map statistics: mean: nan st.d: nan
Map statistics: min: 0, max: 0
/sw/bin/coot: line 5: 66873 Segmentation fault /sw64/bin/coot-
real "$@"
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
