This looks like this: http://biop.ox.ac.uk/coot/doc/coot-faq.html#I-get-bizarre-connectivity-and-other-weirdness-on-reading-files
So you have to set LANG. B
Dear All I recently installed coot 0.7 (Crystallographic molecular graphics (0.7-pre-1-632)) using fink on Mac OSX 10.7.2. The installation run successfully and coot starts without error message. When I open a PDB file, a "Fix Nomenclature Error" window appears with the message "Molecule has 0 Nomenclature Errors"and the PDB file is displayed in a very odd way. Backbone atoms are not connected correctly (see attachement). I tried to install some older builds from wgscott (http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Crystallography_on_OS_X) but these builds behaved the same way. Thanks a lot for your help, Jonas TERMINAL: DEBUG:: filename: /Users/jbarandun/3fms.pdb (handle-read-draw-molecule-with-recentre "/Users/jbarandun/3fms.pdb" 1) Reading coordinate file: /Users/jbarandun/3fms.pdb PDB file /Users/jbarandun/3fms.pdb has been read. Spacegroup: C 1 2 1 Cell: 85 71 43 90 104 90 INFO:: Found 1 models Model 1 had 8 links Symmetry available for this molecule Molecule 0 read successfully Debug:: there were 3 types with no dictionary NI ACT ACT debug:: sbase dictionary for ACT succssfully loaded debug:: sbase dictionary for ACT succssfully loaded INFO:: backup file coot-backup/_Users_jbarandun_3fms.pdb_Mon_Nov_21_08:22:33_2011_modification_0.pdb.gz INFO:: found bad VAL chiral atom: A 6 CB INFO:: (result) ASP swapped atoms in [spec: "A" 7 ""] ASP INFO:: found bad LEU chiral atom: A 37 CG INFO:: (result) ASP swapped atoms in [spec: "A" 75 ""] ASP INFO:: 4 residues had their atoms swapped
-- *************************************************** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: [email protected]
