Hi,
I can also report that with 0.9-pre (the latest CCPEM binaries) I have
occasional crashes when refining. I'm also working on RNA and the crashes seem
to happen when I pull a lot in my structure and generate pull restraints. I
cannot, however, deterministically reproduce the crashes. Below, I've pasted in
a bit of output by coot just before the latest crash.
Regards,
Daniel
...
---------- debug:: in generate_molecule_and_refine() calling
restraints.make_restraints() with imol 0 0 0
INFO:: created 295 restraints
created 102 bond restraints
created 175 angle restraints
created 6 plane restraints
created 12 chiral vol restraints
INFO:: making link polymer links
Made 2 link bond restraints
Made 8 link angle restraints
Made 0 link plane restraints
Made 0 link trans-peptide restraints
INFO:: making flanking restraints
Made 2 flank bond restraints
Made 8 flank angle restraints
Made 0 flank plane restraints
Made 0 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(): 1 start-stop-reserve: 0 start-stop-push: 0 milliseconds
------------------ timings: non-bonded contacts 1 dispatching threads: 0
waiting: 10 adding NBCs to restraints 1
------------------ timings: for make_restraints_ng(): monomers: 0 links: 1
flank: 0 raic: 0 nbc: 14 milliseconds
INFO:: added 0 helical restraints
INFO:: Timing for auto-helix 4 microseconds
------------------ timings: for paired_residues(): 0 0 4 0 0
Made 0 base pairing Hydrogen bonds
--------------------- in add_extra_restraints() 7068 standard restraints
--------------------- in add_extra_restraints() adding 0 extra bond restraints
--------------------- in add_extra_restraints() adding 0 extra angle restraints
--------------------- in add_extra_restraints() par-plan adding 1 pp restraints
--------------------- in add_extra_restraints() target-position adding 0
position restraints
------------------ timings: for make_restraints_ng(): stacking and pairing: 0 5
0 0 ms
:::: make-restraints: analysis of bad geometry in input model
INFO:: Model: Bad Bond: [spec: model 1 "I" 198 "" " O3'" ""] to [spec: model 1
"I" 199 "" " P " ""] nZ 4.065 delta 0.0813 target 1.6 sigma 0.02 distortion
16.53
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "I" 196 "" " O5'" ""] to
[spec: model 1 "I" 195 "" " H3'" ""] delta -0.8167 target 3.04 distortion
14.46
INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "I" 196 "" " P " ""] to
[spec: model 1 "I" 195 "" " H3'" ""] delta -0.9238 target 3.6 distortion 11.67
Refinement elapsed time: 0.902
Key 116 not found in (scheme) key bindings
Minimum found (iteration number 10) at -3411
Final Estimated RMS Z Scores:
bonds: 0.3981
angles: 0.8262
torsions: N/A
trans-peptide: N/A
planes: 0.4226
non-bonded: -0.1205
chiral vol: 0.4
rama plot: N/A
start_pos: N/A
TargetPos: N/A
GemanMcCl: N/A
DEBUG:: ---- free/delete/reset m_s and x
Minimum found (iteration number 14) at -185.7
Final Estimated RMS Z Scores:
bonds: 0.4022
angles: 0.9285
torsions: N/A
trans-peptide: N/A
planes: 3.187
non-bonded: -0.0155
chiral vol: 0.4095
rama plot: N/A
start_pos: N/A
target_pos: 2299 (non-sqrt)
GemanMcCl: N/A
DEBUG:: ---- free/delete/reset m_s and x
Minimum found (iteration number 10) at -3224
Final Estimated RMS Z Scores:
bonds: 0.3977
angles: 0.8807
torsions: N/A
trans-peptide: N/A
planes: 0.5922
non-bonded: -0.102
chiral vol: 0.4212
rama plot: N/A
start_pos: N/A
TargetPos: N/A
GemanMcCl: N/A
DEBUG:: ---- free/delete/reset m_s and x
/Users/larsson/software/ccpem-20191029/bin/coot: line 329: 51480 Segmentation
fault: 11 $coot_bin "$@"
On 2019-11-07, at 11:02, Victor Tobiasson
<[email protected]<mailto:[email protected]>> wrote:
Hello everyone,
I am currently using Coot 0.9-pre through ccpem (git version 1.3.0-84-g605be75)
with CCP4-7.0.077. I am running into a consistent issue with user defined
restraints together with refine_zone() but not with
sphere_refine_regularize_generic(). Whenever I add distance restraints, either
manually or through ideal RNA A form restraints coot crashes immediately upon
setting up restraints through refine_zone(). Coot gives the following terminal
output after immediately after crashing:
(1) " C1'"/1/chainid="CA"/381/U, occ: 1 with B-factor: 13.85 element: " C" at
(343.3,337,314.1) : 0.1057
INFO applying #<procedure #f (atom-specs)> on ((1 1 "CA" 381 "" " C1'" ""))
Backtrace:
In unknown file:
?: 0* [#<procedure #f (atom-specs)> (({1} {1} "CA" 381 "" " C1'" ""))]
In
/home/victor/.local/ccpem-20190901/share/coot/scheme/user-define-restraints.scm:
148: {1}* (let ((spec-1 #) (spec-2 #)) (let (# #) (if # #) (if # #) ...))
149: 2* [list-ref (({1} {1} "CA" 381 "" " C1'" "")) {1}]
/home/victor/.local/ccpem-20190901/share/coot/scheme/user-define-restraints.scm:149:39:
In procedure list-ref in expression (list-ref atom-specs 1):
/home/victor/.local/ccpem-20190901/share/coot/scheme/user-define-restraints.scm:149:39:
Argument 2 out of range: 1
The error is consistent but does not trigger when using
sphere_refine_regularize_generic() where everything works as ahould be. This
problem has been with me for a while now has existed throughout several
versions and installs. This is the error for Coot version 0.8.9.2-pre nightly
build 7766:
(1) " N1 "/1/chainid="CA"/584/G, occ: 1 with B-factor: 16.32 element: " N" at
(352.5,322.5,325) : 0.3861
INFO applying #<procedure #f (atom-specs)> on ((1 1 "CA" 584 "" " N1 " ""))
Backtrace:
In unknown file:
?: 0* [#<procedure #f (atom-specs)> (({1} {1} "CA" 584 "" " N1 " ""))]
In /home/victor/.local/coot_231019/share/coot/scheme/user-define-restraints.scm:
148: {1}* (let ((spec-1 #) (spec-2 #)) (let (# #) (if # #) (if # #) ...))
149: 2* [list-ref (({1} {1} "CA" 584 "" " N1 " "")) {1}]
/home/victor/.local/coot_231019/share/coot/scheme/user-define-restraints.scm:149:39:
In procedure list-ref in expression (list-ref atom-specs 1):
/home/victor/.local/coot_231019/share/coot/scheme/user-define-restraints.scm:149:39:
Argument 2 out of range: 1
ObjectCache: Leaked 0001 refs to <P 1 Nuvw = ( 600, 600, 600)>
ObjectCache: Leaked 0001 refs to <P 1>
guile: error while loading shared libraries: libguile.so.17: cannot open shared
object file: No such file or directory
failed to launch the crash catcher
Any ideas? I can of course live without the extra restraints but they make low
resolution RNA modelling so much easier.
Best,
Victor Tobiasson
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