Dear all
When trying to model nucleotides (ATP, FAD, NADH) using the "edit angles" or
"regularise zone" tools in order to optimise fitting , coot crashes with the
following message:
/usr/local/bin/ccp4/ccp4-7.1/bin/coot: line 333: 4997 Segmentation fault
(core dumped) $coot_bin "$@"
;;; note: source file
/usr/local/bin/ccp4/ccp4-7.1/share/guile/1.8/ice-9/boot-9.scm
;;; newer than compiled /usr/lib64/guile/2.0/ccache/ice-9/boot-9.go
Throw without catch before boot:
Throw to key syntax-error with args ("memoization" "In file ~S, line ~S: ~A
~S." ("/usr/local/bin/ccp4/ccp4-7.1/share/guile/1.8/ice-9/boot-9.scm" 101 "Bad
define placement" (define (toplevel-env? env) (or (not (pair? env)) (not (pair?
(car env)))))) #f)Aborting.
/usr/local/bin/ccp4/ccp4-7.1/bin/coot: line 333: 5428 Aborted
(core dumped) guile --version
failed to launch the crash catcher
I'm using coot 0.9:
0.9 (revision-count 9932)
[with guile 1.8.8 embedded]
[with python 2.7.16 embedded]
Builder_info: CCP4, Oxfordshire
Binary type: Linux-x86_64-scientific-linux-6.10-python-gtk2
Enabled: Enhanced-ligand-tools C++-11 Threads Boost-based-thread-pool Goocanvas
GSL SQLite3 LibCurl
Builder_info: CCP4, Oxfordshire
No session info is saved so I have to redo all previous work. There is no map,
it's in silico modelling being based on superposition with known, homologous
ATP-protein complexes and using the phosphate positions as a guide.
Any suggestions what might be the problem and how to solve the issue?
Many thanks!
Paula
===================================
Dr Paula S. Salgado
Senior Lecturer in Macromolecular Crystallography
Molecular Mechanisms of Life Lead
During the current COVID-19 crisis, my working hours tend to focus on early
afternoons and evenings, so please bear with me if my reply is delayed and if I
email outside your normal working hours. In any case, I do not expect a
response outside those hours. Stay home if you're not involved in essential
work, stay safe.
Newcastle University Biosciences Institute
Faculty of Medical Sciences
2nd Floor Cookson Building
Newcastle University
Newcastle upon Tyne, NE2 4HH, UK
Tel: +44 (0)191 208 7432
Email: [email protected]
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