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    Ghemical: Molecular modelling - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #54 ] MM1 Ribbon crashes
    Date:
    11/15/01 11:29
    Submitted by:
    hutchisn     		Assigned to:
    unset
    Category:
    MM1 Mode     		Priority:
    5
    Ticket group:
    Fixed     		Resolution:
    Unset
    Summary:
    MM1 Ribbon crashes
    Original submission:
    Reading CobraToxin.pdb

    nmol = 1
    1 chains:

    (crash)

    0x405a8989 in __wait4 () from /lib/i686/libc.so.6
    #0 0x405a8989 in __wait4 () from /lib/i686/libc.so.6
    #1 0x40624534 in __DTOR_END__ () from /lib/i686/libc.so.6
    #2 0x403a6e88 in gnome_segv_handle () from /usr/lib/libgnomeui.so.32
    #3 <signal handler called>
    #4 mm1_sequencebuilder::BuildTemplate (this=0x8bffd60, tdata=@0xbfffeba0,
    adata=@0xa90df40) at /usr/include/g++-3/stl_vector.h:218
    #5 0x080e9920 in mm1_sequencebuilder::Identify (this=0x8bffd60, mdl=0xab194a8)
    at /home/hutchisn/src/ghemical/src/common/mm1util.cpp:912
    #6 0x080b4393 in gnome_mm1_docv::popup_ObjRibbon (data=0xab249f8)
    at /home/hutchisn/src/ghemical/src/target3/t3mm1docv.cpp:673
    Please log in to add comments and receive followups via email.
    Followups
    Comment Date By
    I've experienced this bug too.It seems that the algorithm can't identify the terminal amino acid if hydrogens are added. Meaning ARNDCQE becomes ARNDCQ?. This seems to be the root of the problem.

    The crash occurs in the for loop at line 920 in mm1util.cpp. when residue_vector[tmp1[0]].id is referenced. For the amino acid that is not identified tmp1[0]=-1. This causes the segfault. Putting an if(tmp[0]!=-1) { ... } at the
    start of the for loop seems to be a functional workaround, but the real problem is not being able to identify the terminal amino acid with hydrogens, and I don't have any idea of how to fix that.     		07/22/02 04:10 crowley
    I've experienced this bug too.It seems that the algorithm can't identify the terminal amino acid if hydrogens are added. Meaning ARNDCQE becomes ARNDCQ?. This seems to be the root of the problem.

    The crash occurs in the for loop at line 920 in mm1util.cpp. when residue_vector[tmp1[0]].id is referenced. For the amino acid that is not identified tmp1[0]=-1. This causes the segfault. Putting an if(tmp[0]!=-1) { ... } at the
    start of the for loop seems to be a functional workaround, but the real problem is not being able to identify the terminal amino acid with hydrogens, and I don't have any idea of how to fix that.     		07/22/02 02:09 crowley
    Before drawing a ribbon, it tries to identify the chains and sequence.

    That's where the problem seems to be. I was able to repeat this, but I'm afraid I can't fix this anytime soon. All I can say is the ribbons work with "clean" examples like the ones built with the sequence builder... :(
    		12/05/01 08:41 thassine
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    Ticket change history
    Field Old value Date By
    status_id Unset 03/30/06 16:29 hutchisn
    bug_group_id Need Info 03/30/06 16:29 hutchisn
    close_date 12/31/69 19:00 03/30/06 16:29 hutchisn

     
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