Ah, interesting. What is the name of the directory that you had been
running it in?
Paul.
On Tue, 2007-05-15 at 18:51 +0100, Eric Tee wrote:
> Hi Paul,
> Thanks for your reply. The problem can be "avoided" (instead of
> solved) by initiating coot from the home directory rather than working
> directory. Below are what I got from home and working directories when
> I mutate met to leu:
>
> >From home directory (successful case):
> INFO:: mutate 94 A to a LEU
> INFO:: backup file
> coot-backup/_home_Tee_Desktop_d_drive_ccp4_data_nat2_model4.pdb_Tue_May_15_18:24:08_2007_modification_0.pdb.gz
> ==== fitting residue 94 A to map number 1 ======
> debug afbr probabilities.size() 4 1
> INFO:: backup file
> coot-backup/_home_Tee_Desktop_d_drive_ccp4_data_nat2_model4.pdb_Tue_May_15_18:24:08_2007_modification_1.pdb.gz
> 8 atoms updated.
>
> >From working directory (fail):
> INFO:: mutate 94 A to a LEU
> INFO:: backup file
> coot-backup/_mnt_d_drive_ccp4_data_nat2_model4.pdb_Tue_May_15_18:31:53_2007_modification_0.pdb.gz
> sh:
> coot-backup/_mnt_d_drive_ccp4_data_nat2_model4.pdb_Tue_May_15_18:31:53_2007_modification_0.pdb.gz: Invalid argument
>
> Gtk-WARNING **: Unable to locate loadable module in module_path:
> "libraleigh.so",
> coot-exe: "/home/Tee/programs/ccp4/Coot-0.3.1/bin/coot-real"
> core: #f
> /usr/bin/gdb
> ERROR: In procedure execlp:
> ERROR: Wrong type argument in position 2: (#f)
>
> However, I can continue with my refinement.
>
> Regards,
> Eric
>
>
> On 5/14/07, Paul Emsley <[log in to unmask]> wrote:
> On Sun, 2007-05-13 at 13:05 +0100, wrote:
>
> > I tried to mutate a met to ala using "mutate & auto fit" but
> when I click on
> > "ALA" after selecting a map, Coot closed automatically and I
> got the
> > following error message from the terminal:
> >
> > INFO:: mutate 140 A to a ALA
> > INFO:: backup file
> >
> coot-backup/_mnt_ccp4_data_nat2_model4_refmac4.pdb_Sun_May_13_12:41:57_2007_modification_0.pdb.gz
> > sh: coot-backup/_mnt_ccp4_data_nat2_model4_refmac4.pdb_Su
> > n_May_13_12:41:57_2007_modification_0.pdb.gz: Invalid
> argument
> >
> > Gtk-WARNING **: Unable to locate loadable module in
> module_path:
> > "libraleigh.so" ,
> > coot-exe:
> "/home/eric/programs/ccp4/Coot-0.3.1/bin/coot-real"
> > core: #f
> > /usr/bin/gdb
> > ERROR: In procedure execlp:
> > ERROR: Wrong type argument in position 2: (#f)
> >
> > Please let me know how to rectify this problem?
>
> Hi Eric.
>
> Oh dear. What you are seeing here (mostly) is my fumbled
> attempt to get
> a core dump report. In this case, you don't have a core dump
> and get
> this error.
>
> I can't think at all why Coot should crash where you say it
> did. If we
> could see a backtrace, that'd help a lot. unlimit
> coredumpsize, I
> suspect will do the trick.
>
> Alternatively, if you can reproduce this and can send me the
> data/coords
> (confidentially) then I can track down the problem (probably).
>
> Paul.
>
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