I'm getting a segfault when I try to read structure factors
from a *.cif file downloaded from the wwPDB.
Coot version 0.8.1 from ccp4 6.4.0 (linux)
Here are the messages to the terminal screen leading up to the segfault:
CCP4MTZfile: open_read - File missing or corrupted:
/sgpp/data/process/EtCDPK/1354/1946b4/deposit/D_1000208126_sf-annotate_P1.cif
INFO:: not an mtz file:
/sgpp/data/process/EtCDPK/1354/1946b4/deposit/D_1000208126_sf-annotate_P1.cif
>>>>>> CCP4 library signal mtz:File not identified as MTZ (Error)
raised in MtzGet <<<<<<
CCP4MTZfile: open_read - File missing or corrupted:
/sgpp/data/process/EtCDPK/1354/1946b4/deposit/D_1000208126_sf-annotate_P1.cif
INFO:: not an mtz file:
/sgpp/data/process/EtCDPK/1354/1946b4/deposit/D_1000208126_sf-annotate_P1.cif
INFO:: data file
/sgpp/data/process/EtCDPK/1354/1946b4/deposit/D_1000208126_sf-annotate_P1.cif
is not a valid mtz file
/sgpp/data/process/EtCDPK/1354/1946b4/deposit/D_1000208126_sf-annotate_P1.cif
is not a .phs file
/sgpp/data/process/EtCDPK/1354/1946b4/deposit/D_1000208126_sf-annotate_P1.cif
is a mmCIF file
[segfault]
Here is the backtrace:
Program received signal SIGSEGV, Segmentation fault.
0xb61d555d in clipper::CIFfile::close_read() ()
from /sgpp/CCP4/ccp4-6.5/libexec/../lib/libclipper-cif.so.2
(gdb) where
#0 0xb61d555d in clipper::CIFfile::close_read() ()
from /sgpp/CCP4/ccp4-6.5/libexec/../lib/libclipper-cif.so.2
#1 0x0872a8f3 in molecule_class_info_t::make_map_from_cif_sigmaa(int,
std::string, int) ()
#2 0x0872a758 in molecule_class_info_t::make_map_from_cif(int, std::string) ()
#3 0x084fc426 in read_cif_data_with_phases_sigmaa ()
#4 0x084fc2e7 in auto_read_cif_data_with_phases ()
#5 0x0851af0e in coot::column_selector_using_cmtz(std::string const&) ()
#6 0x08422721 in manage_column_selector ()
#7 0x08507401 in on_ok_button_dataset_clicked ()
#8 0xb444f9a3 in g_cclosure_marshal_VOID__VOID ()
from /sgpp/CCP4/ccp4-6.5/libexec/../lib/libgobject-2.0.so.0
#9 0xb444dc0e in g_closure_invoke ()
from /sgpp/CCP4/ccp4-6.5/libexec/../lib/libgobject-2.0.so.0
#10 0xb445f789 in signal_emit_unlocked_R ()
from /sgpp/CCP4/ccp4-6.5/libexec/../lib/libgobject-2.0.so.0
#11 0xb4467b10 in g_signal_emit_valist ()
[snip a ton of stuff internal to gtk]
#33 0xb4344b58 in g_main_context_iterate.isra.22 ()
from /sgpp/CCP4/ccp4-6.5/libexec/../lib/libglib-2.0.so.0
#34 0xb4344f7b in g_main_loop_run ()
from /sgpp/CCP4/ccp4-6.5/libexec/../lib/libglib-2.0.so.0
#35 0xb4ab1c20 in gtk_main () from
/sgpp/CCP4/ccp4-6.5/libexec/../lib/libgtk-x11-2.0.so.0
#36 0x083d1535 in c_inner_main ()
#37 0xb6373f84 in invoke_main_func () from
/sgpp/CCP4/ccp4-6.5/libexec/../lib/libguile.so.17
#38 0xb6341b70 in c_body () from
/sgpp/CCP4/ccp4-6.5/libexec/../lib/libguile.so.17
#39 0xb63c2547 in scm_c_catch () from
/sgpp/CCP4/ccp4-6.5/libexec/../lib/libguile.so.17
#40 0xb63421cf in scm_i_with_continuation_barrier ()
from /sgpp/CCP4/ccp4-6.5/libexec/../lib/libguile.so.17
#41 0xb63422a5 in scm_c_with_continuation_barrier ()
from /sgpp/CCP4/ccp4-6.5/libexec/../lib/libguile.so.17
#42 0xb63bff43 in scm_i_with_guile_and_parent ()
from /sgpp/CCP4/ccp4-6.5/libexec/../lib/libguile.so.17
#43 0xb63c000d in scm_with_guile () from
/sgpp/CCP4/ccp4-6.5/libexec/../lib/libguile.so.17
---Type <return> to continue, or q <return> to quit---
#44 0xb63740e5 in scm_boot_guile () from
/sgpp/CCP4/ccp4-6.5/libexec/../lib/libguile.so.17
#45 0x083d16c7 in c_wrapper_scm_boot_guile ()
#46 0x083c1382 in main ()
cif2mtz via ccp4i has no problem processing this file,
other than the usual annoyance that it ignores the cell
parameters at the top of the file so you have to type
them in via the interface. Although come to think of it,
maybe this is the same issue with coot (not reading the
cell parameters)?
Here is the top of the *.cif file:
data_r4yuqsf
#
_audit.revision_id 1
_audit.creation_date 2015-03-18
_audit.update_record ?
#
_cell.entry_id 4yuq
_cell.length_a 68.7010
_cell.length_b 94.2530
_cell.length_c 87.3950
_cell.angle_alpha 90.0000
_cell.angle_beta 93.0600
_cell.angle_gamma 90.0000
#
_diffrn.id 1
_diffrn.crystal_id 1
_diffrn.ambient_temp ?
_diffrn.crystal_treatment ?
_diffrn.details ?
#
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 0.97945
#
#
_diffrn_reflns.diffrn_id 1
_diffrn_reflns.pdbx_d_res_high 2.777
_diffrn_reflns.pdbx_d_res_low 87.270
_diffrn_reflns.limit_h_max 24
_diffrn_reflns.limit_h_min -24
_diffrn_reflns.limit_k_max 33
_diffrn_reflns.limit_k_min 0
_diffrn_reflns.limit_l_max 31
_diffrn_reflns.limit_l_min 0
_diffrn_reflns.number 28063
_diffrn_reflns.pdbx_number_obs 26663
#
_entry.id 4yuq
#
_exptl_crystal.id 1
#
_reflns_scale.group_code 1
#
_symmetry.entry_id 4yuq
_symmetry.space_group_name_H-M 'P 1 21 1'
_symmetry.Int_Tables_number 4
#
loop_
_symmetry_equiv.id
_symmetry_equiv.pos_as_xyz
1 'X, Y, Z'
2 '-X, Y+1/2, -Z'
#
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.F_meas_au
_refln.F_meas_sigma_au
_refln.F_calc
_refln.phase_calc
_refln.phase_meas
_refln.pdbx_I_plus
_refln.pdbx_I_plus_sigma
_refln.pdbx_I_minus
_refln.pdbx_I_minus_sigma
_refln.pdbx_anom_difference
_refln.pdbx_anom_difference_sigma
_refln.fom
1 1 1 -24 0 1 o 176.936 84.696 16.411 180.000 180.000 5.7000 3.0000
5.7000 3.0000 0.000000 0.000000 0.19
1 1 1 -24 0 2 o 116.289 78.687 10.061 0.0000 0.0000 2.2000 4.7000
2.2000 4.7000 -0.000000 0.000000 0.08
1 1 1 -24 0 3 x ? ? 35.230 0.0000 0.0000 ? ? ? ?
? ? 0.00
1 1 1 -24 0 4 x ? ? 11.609 180.000 180.000 ? ? ? ?
? ? 0.00
1 1 1 -24 0 5 o 79.035 55.231 16.288 0.0000 0.0000 -0.6000 2.8000
-0.6000 2.8000 0.000000 0.000000 0.10
1 1 1 -24 0 6 o 88.099 60.212 9.0507 0.0000 0.0000 0.8000 2.9000
0.8000 2.9000 -0.000000 0.000000 0.06
1 1 1 -24 0 7 o 98.340 66.921 23.930 0.0000 0.0000 2.3000 3.5000
2.3000 3.5000 -0.000000 0.000000 0.16
[...]
cheers,
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
