While most (all?) CCP4 programs use the MMDB library for reading PDB files, handling of incorrect PDBs is not consistent. Default settings in MMDB (and in clipper) are strict, but most of the programs use a combination of options that make it more liberal (SetFlag()).
Marcin On Mon, Jan 12, 2015 at 04:28:07PM +0000, Jon Agirre wrote: > Hi Jan, > > Privateer relies on Clipper-minimol, which in turn uses MMDB. According to > MMDB's error code description list ( > https://www.ebi.ac.uk/pdbe/docs/cldoc/object/cl_obj_irets.html) : > > Error_WrongEntryID 3 A PDB or mmCIF record that ought to display > this entry's ID, shows an ID contradicting to that in header. > > I've been able to replicate the error by opening a PDB file downloaded from > PDBe and changing the HEADER line to show a different PDB ID. Is that your > case? > > Thanks for your interest, > > Jon > > On 12 January 2015 at 15:59, Jan Stransky <jan.stransky.c...@gmail.com> > wrote: > > > Dear all, > > I am experiencing some troubles with running Privateer. It seems to fail > > to read a PDB file. The Error message: > > > > Reading xxx.pdb... MMDBfile: read_file error: xxx.pdb : 3 > > terminate called after throwing an instance of 'clipper::Message_fatal' > > Aborted > > > > Any ideas? > > Best regards, > > Jan > > > > > > -- > Dr Jon Agirre > York Structural Biology Laboratory / Department of Chemistry > University of York, Heslington, YO10 5DD, York, England > http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/ > +44 (0) 1904 32 8253 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
