On 24/03/14 22:14, Ming Sun wrote:
Hi All
I'm currently having problems in "undo". Whenever I click undo after
align_and_mutate(), Coot will be closed automatically.
(coot-0.8-pre-revision-4942, OpenSUSE-12.3)
I am new to coot. Does it happen to anyone else? I copied the
original error message here. Thanks again
INFO:: backup file
coot-backup/_data_ming_Coot_CCP4_refine.pdb_Mon_Mar_24_16:07:46_2014_modification_48.pdb.gz
restoring from backup 49 49
Reading coordinate file:
coot-backup/_data_ming_Coot_CCP4_refine_coot-coot-0.pdb_Mon_Mar_24_16:07:46_2014_modification_47.pdb.gz
gzip: stdout: Broken pipe
gzip: stdout: Broken pipe
gzip: stdout: Broken pipe
There was an error reading
coot-backup/_data_ming_Plasmodium_Coot_CCP4_refine_coot-coot-0.pdb_Mon_Mar_24_16:07:46_2014_modification_47.pdb.gz.
ERROR 39 READ: Duplicate sequence number and insertion code.
LINE #9316
ATOM 9310 N PHE D 189 -265.099 147.312 221.215 1.00
20.00 G N
Spacegroup: P 1
There was a coordinates read error
DEBUG:: apply_undo: (end) history_index: 47 max_history_index: 49
/home/ming/data/Programs/coot-0.8/bin/coot: line 259: 4354
Segmentation fault $coot_real "$@"
/data/ming/Programs/coot-0.8/bin/guile: error while loading shared
libraries: libltdl.so.3: cannot open shared object file: No such file
or directory
[1] Exit 139 ~/data/Programs/coot-0.8/bin/coot
Dear Ming Sun,
(Congratulations on using a recent pre-release coot) Thanks for your
feedback.
You have tripped over an esoteric bug - which I will fix shortly - to
stop coot crashing at least (more later).
The important thing for you is this:
Duplicate sequence number and insertion code
LINE #9316 ATOM 9310 N PHE D 189
Coot (now) doesn't like to read PDB files that have different residue
types for a given model, chain-id, residue number and insertion code.
It used to allow this - it no longer does (as it causes instabilities in
the program (ironically enough)).
So if you want to allow coot to read your PDB file you will have to
either remove this typo or handle the micro-heterogeneity (if that is
what you have) using a different model.
Regards,
Paul.
