Dear all, We have encountered some problems when using the carbohydrate module in coot.
When I centre on an Asn which has NAG density, invoke the Carbohydrate module and select "Add ASN-NAG NAG", Coot crashes and dumps the core. The error message displayed in the terminal is as follows: INFO:: recentre: clicked on imol: 0 Elapsed time for map contouring: 31ms INFO:: using standard CCP4 Refmac dictionary to search for "NAG" There are 2 data in /home/public/packages/ccp4-6. 5/lib/data/monomers/n/NAG.cif reading /home/public/packages/ccp4-6.5/share/coot/link-by-torsion- to-pyranose-core-NAG-ASN.tab reading /home/public/packages/ccp4-6.5/share/coot/NAG-decorations.tab INFO:: backup file coot-backup/_home_dave_XXXX_in_house_Morph_Refine_ 19_XXXX_refine_19.pdb_Thu_Jul__9_12:18:56_2015_modification_1.pdb.gz INFO:: backup file coot-backup/_home_dave_XXXX_in_house_Morph_Refine_ 19_XXXX_refine_19.pdb_Thu_Jul__9_12:18:56_2015_modification_2.pdb.gz *** glibc detected *** /home/public/packages/ccp4-6.5/libexec/coot-bin: corrupted double-linked list: 0x0000000005036570 *** ======= Backtrace: ========= /lib64/libc.so.6[0x329d475916] /lib64/libc.so.6[0x329d475d9d] /lib64/libc.so.6[0x329d478bb5] /lib64/libc.so.6(__libc_malloc+0x71)[0x329d47a141] /usr/lib64/libGL.so.1[0x32a74a6955] ======= Memory map: ======== ((Omitted for brevity)) I assume that "*** glibc detected *** /home/public/packages/ccp4-6.5/libexec/coot-bin: corrupted double-linked list: 0x0000000005036570 ***" is the problem, but I am unsure how best to address this. We are running the version of coot 0.8 supplied with the ccp4-6.5 release. This issue can be replicated with different pdbs and mtzs loaded. We are running coot in RHEL 6.3, with Kernel 2.6.32-279.14.1.el6.x86_64 . However - this issue does not present for us when using the same version of coot on OSX. Can anybody suggest a fix? Regards, David [image: David Briggs on about.me] David Briggs about.me/david_briggs <http://about.me/david_briggs>
