Hi Paul Thanks for the reply. Yes. I opened several different pdb models in Coot at the same time. Could it be possible that after align_and_mutate, that specific atom has duplicate coordinate with atoms in other pdb model. If it's the case, I will use only one model at one time and go to the other one later.
Thanks -Ming On Wed, Mar 26, 2014 at 11:42 AM, Paul Emsley <[email protected]>wrote: > > 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. > > -- Ming Sun Columbia University (E): [email protected]
