Hi all
I don't know if this segfault is of use...
---------- Forwarded message ---------
From: Theodor Everley Röhrkasten <ter...@york.ac.uk>
Date: Wed, 17 Mar 2021 at 12:32
Subject: Segfault again
To: Kevin Cowtan <kevin.cow...@york.ac.uk>
Somehow I appeared to be in Rigid Body Fit mode, but there was no dialog
box and I couldn't exit the mode. I tried to use Real Space Refine, and
Coot crashed. I'm not sure how far back to go, so some of this might be
irrelevant. Also, I think in the crash report at the end, it's supposed
to be printing the output of uname and ls, not the paths of the binaries.
Here's my uname, in case it helps: Linux p50 5.11.2-1-default #1 SMP Fri
Feb 26 10:11:13 UTC 2021 (ee0b277) x86_64 x86_64 x86_64 GNU/Linux
Begin output:
----------------------- FAIL, ENOPROG ---------------
DEBUG:: ---- free/delete/reset m_s and x
addition of target position restraints: pre and post sizes: 682 683
debug:: thread_for_refinement_loop_threaded() restraints locked by
refinement_loop_threaded
INFO:: Clear pull restraint on atom: [spec: model 1 "A" 2 "" " CA " ""]
debug:: thread_for_refinement_loop_threaded() restraints locked by
refinement_loop_threaded
Minimum found (iteration number 2) at -4.21e+03
Final Estimated RMS Z Scores:
bonds: 1.02
angles: 2.39
improper-dihedrals: N/A
torsions: N/A
trans-peptide: 19.4 (non-sqrt)
planes: 0.852 from 7 restraints
parallel planes: N/A
non-bonded: -0.532
chiral vol: 1.39
rama plot: N/A
start_pos: N/A
target_pos: 0 (non-sqrt)
GemanMcCl: N/A
DEBUG:: ---- free/delete/reset m_s and x
INFO:: backup file name
coot-backup/coot-refmac_model_refmac0_refmac1.pdb_Wed_Mar_17_12:35:42_2021_modification_6.pdb.gz
INFO:: replace_coords: 21 atoms updated.
debug:: in clear_all_atom_pull_restraints() 0
click on 2 atoms to define a zone
(do-rot-trans-setup 1)
click on an atom of a terminal residue
(do-add-terminal-residue 1)
(7) " CA "/1/chainid="A"/2/SER, AA occ: 1 with B-factor: 58.8 element: "
C" at (-26.4,33.2,2.74) : 0.0922
(7) " CA "/1/chainid="A"/2/SER, AA occ: 1 with B-factor: 58.8 element: "
C" at (-26.4,33.2,2.74) : 0.0922
INFO:: fitting terminal residue with 5000 random trials
WARNING:: No symmetry available for this molecule
WARNING:: No Symmetry for this model
INFO:: done mutating residue [spec: 1 "A" 1 ""] in add_cb_to_terminal_res
INFO:: backup file name
coot-backup/coot-refmac_model_refmac0_refmac1.pdb_Wed_Mar_17_12:35:42_2021_modification_7.pdb.gz
(do-add-terminal-residue 0)
(7) " OG "/1/chainid="A"/2/SER, AA occ: 1 with B-factor: 60.6 element: "
O" at (-26.8,31.1,1.59) : 0.13
(7) " CB "/1/chainid="A"/2/SER, AA occ: 1 with B-factor: 58.2 element: "
C" at (-26.6,31.7,2.86) : 0.114
(7) " C "/1/chainid="A"/2/SER, AA occ: 1 with B-factor: 57.1 element: "
C" at (-25,33.6,2.22) : 0.124
(7) " CA "/1/chainid="A"/3/THR, AA occ: 1 with B-factor: 49.6 element: "
C" at (-23.4,33.6,0.408) : 0.0896
(7) " OD1"/1/chainid="A"/4/ASP, AA occ: 1 with B-factor: 31 element: "
O" at (-23,37,3.3) : 0.316
DEBUG:: in find_atom_in_moving_atoms: here are the 1 qualifying atoms...
0 1/A/4 {ASP}/ OD1 altLoc :: segid :AA: pos: (-23,37,3.3)
B-factor: 31
DEBUG:: not doing refinement - no restraints.
(rot-trans-reset-previous)
INFO:: backup file name
coot-backup/coot-refmac_model_refmac0_refmac1.pdb_Wed_Mar_17_12:35:42_2021_modification_8.pdb.gz
restoring from backup 9 9
INFO:: Reading coordinate file:
coot-backup/coot-refmac_model_refmac0_refmac1.pdb_Wed_Mar_17_12:35:42_2021_modification_7.pdb.gz
INFO:: file
coot-backup/coot-refmac_model_refmac0_refmac1.pdb_Wed_Mar_17_12:35:42_2021_modification_7.pdb.gz
has been read.
Spacegroup: P 61
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
DEBUG:: apply_undo: (end) history_index: 7 max_history_index: 9
(apply-undo)
restoring from backup 9 7
INFO:: Reading coordinate file:
coot-backup/coot-refmac_model_refmac0_refmac1.pdb_Wed_Mar_17_12:35:42_2021_modification_8.pdb.gz
INFO:: file
coot-backup/coot-refmac_model_refmac0_refmac1.pdb_Wed_Mar_17_12:35:42_2021_modification_8.pdb.gz
has been read.
Spacegroup: P 61
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
(apply-redo)
click on 2 atoms to define a zone
(do-rot-trans-setup 1)
DEBUG:: not doing refinement - no restraints.
restoring from backup 9 8
INFO:: Reading coordinate file:
coot-backup/coot-refmac_model_refmac0_refmac1.pdb_Wed_Mar_17_12:35:42_2021_modification_7.pdb.gz
INFO:: file
coot-backup/coot-refmac_model_refmac0_refmac1.pdb_Wed_Mar_17_12:35:42_2021_modification_7.pdb.gz
has been read.
Spacegroup: P 61
INFO:: Found 1 models
Model 1 had 0 links
in add_molecular_symmetry_matrices() made 0 biomt matrices
DEBUG:: apply_undo: (end) history_index: 7 max_history_index: 9
(apply-undo)
(set-delete-residue-mode)
DEBUG:: not doing refinement - no restraints.
(clear-pending-delete-item)
Pending Picks Cleared
(clear-pending-delete-item)
Pending Picks Cleared
DEBUG:: not doing refinement - no restraints.
DEBUG:: not doing refinement - no restraints.
DEBUG:: not doing refinement - no restraints.
click on 2 atoms (in the same molecule)
DEBUG:: erasing moving atoms dragged atom with index: 16
(7) " C "/1/chainid="A"/2/SER, AA occ: 1 with B-factor: 57.1 element: "
C" at (-25,33.6,2.22) : 0.153
(7) " C "/1/chainid="A"/2/SER, AA occ: 1 with B-factor: 57.1 element: "
C" at (-25,33.6,2.22) : 0.159
(7) " C "/1/chainid="A"/2/SER, AA occ: 1 with B-factor: 57.1 element: "
C" at (-25,33.6,2.22) : 0.159
returning an atom selection for all moving atoms 6 atoms
INFO:: from_res_vec() created 11 monomer restraints
created 5 bond restraints
created 5 angle restraints
created 0 plane restraints
created 1 chiral vol restraints
created 0 improper dihedral restraints
INFO:: making link polymer links
Made 0 link bond restraints
Made 0 link angle restraints
Made 0 link plane restraints
Made 0 link trans-peptide restraints
Made 1 flank bond restraints
Made 3 flank angle restraints
Made 2 flank plane restraints
Made 1 flank trans-peptide restraints
Made 0 CHO-SS-and-other bond restraints
Made 0 CHO-SS-and-other angle restraints
Made 0 CHO-SS-and-other plane restraints
Made 0 CHO-SS-and-other trans-peptide restraints
------------------ timings: for make_link_restraints_ng(): polymers: 0
flanking: 0 others: 0 milliseconds
------------------ timings: make_non_bonded_contact_restraints_ng():
energy types 0 milliseconds
------------------ timings: make_non_bonded_contact_restraints_ng():
find_the_contacts(): 0 start-stop-reserve: 0 start-stop-push: 0 milliseconds
------------------ timings: non-bonded contacts 0 dispatching threads: 0
waiting: 10 adding NBCs to restraints 0
------------------ timings: for make_restraints_ng(): monomers: 0 links:
1 flank: 0 raic: 0 nbc: 11 milliseconds
INFO:: added 0 helical restraints
INFO:: Timing for auto-helix 8 microseconds
------------------ timings: for paired_residues(): 0 0 2 0 0
INFO:: Made 0 base pairing Hydrogen bonds
------------------ timings: for make_restraints_ng(): stacking and
pairing: 0 2 0 0 ms
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 2 "" " O "
""] to [spec: model 1 "A" 42 "" " NE1" ""] delta -0.401 target 3.12
distortion 23.4
Stack trace (most recent call last) in thread 30044:
#7 Object "[0xffffffffffffffff]", at 0xffffffffffffffff, in
#6 Object "/lib64/libc.so.6", at 0x7f84573adaf2, in clone
#5 Object "/lib64/libpthread.so.0", at 0x7f845f06e298, in
#4 Object "/usr/lib64/libstdc++.so.6", at 0x7f8457702191, in
#3 Object "/opt/xtal/ccp4-7.1/libexec/coot-bin", at 0x7f5311, in
graphics_info_t::refinement_loop_threaded()
#2 Object "/opt/xtal/ccp4-7.1/libexec/coot-bin", at 0x7e6e3d, in
graphics_info_t::update_restraints_with_atom_pull_restraints()
#1 Object "/opt/xtal/ccp4-7.1/libexec/coot-bin", at 0x5ffef5, in
coot::atom_spec_t::atom_spec_t(mmdb::Atom*)
#0 Object "/opt/xtal/ccp4-7.1/libexec/../lib/libmmdb2.so.0", at
0x7f845f1041fc, in mmdb::Atom::GetChainID()
Segmentation fault (Signal sent by the kernel [(nil)])
/opt/xtal/ccp4-7.1/bin/coot: line 339: 26881 Segmentation fault
(core dumped) $coot_bin "$@"
. ------ Coot crashed - trying to diagnose -----
ldd -r on guile gives:
linux-vdso.so.1 (0x00007ffcdd5f6000)
libguile.so.17 =>
/opt/xtal/ccp4-7.1/libexec/../lib/libguile.so.17 (0x00007f39d9a22000)
libgmp.so.10 => /opt/xtal/ccp4-7.1/libexec/../lib/libgmp.so.10
(0x00007f39d97a1000)
libcrypt.so.1 => /usr/lib64/libcrypt.so.1 (0x00007f39d974a000)
libm.so.6 => /lib64/libm.so.6 (0x00007f39d9605000)
libltdl.so.7 => /opt/xtal/ccp4-7.1/libexec/../lib/libltdl.so.7
(0x00007f39d93fb000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f39d93da000)
libc.so.6 => /lib64/libc.so.6 (0x00007f39d9209000)
/lib64/ld-linux-x86-64.so.2 (0x00007f39d9d26000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f39d9202000)
Guile 1.8.8
Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005,
2006, 2007, 2008 Free Software Foundation
Guile may be distributed under the terms of the GNU General Public Licence;
certain other uses are permitted as well. For details, see the file
`COPYING', which is included in the Guile distribution.
There is no warranty, to the extent permitted by law.
catching the crash log:
Gtk-Message: Failed to load module "canberra-gtk-module"
coot-exe: "/opt/xtal/ccp4-7.1/libexec/coot-bin"
/usr/bin/ls
coot-version:
/opt/xtal/ccp4-7.1/libexec/coot-bin
platform:
/usr/bin/uname
core: #f
No core file found. No debugging
--
Professor Kevin Cowtan
Email: kevin.cow...@york.ac.uk
Pronouns: Please use he/him or they/them when referring to me in
professional contexts
Address: York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD: 0000-0002-0189-1437 <https://orcid.org/0000-0002-0189-1437>
Web: https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
Disclaimer: http://w <http://www.york.ac.uk/docs/disclaimer/email.htm>
ww.york.ac.uk/docs/disclaimer/email.htm
<http://www.york.ac.uk/docs/disclaimer/email.htm>
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