Thanks for the neat command line! In fact the MolProbity web server can handle the original file as well as the 'timmed' file, so this seems to be a peculiarity in the implementation in coot (win7.2.1) in which neither works. I did download the latest reduce/probe, btw. I'll dig more. Thx, BR
-----Original Message----- From: Tim Gruene [mailto:[email protected]] Sent: Mittwoch, 21. Mai 2014 14:54 To: [email protected]; [email protected] Subject: Re: [ccp4bb] Minimum requirements for validation/coot/probe/ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Bernhard, I am not sure this represents your problem: when I only select the ATOM cards and of those only columns 1-56 grep "^ATOM" 9INS.pdb | cut -c 1-56 > 9INS_coords.pdb the molprobity server has no problems analysing this file including the addition of hydrogen atoms. The PDB-file has lines such as ATOM 433 N LYS B 29 15.668 49.766 24.933 ATOM 434 CA LYS B 29 14.854 50.940 25.268 ATOM 435 C LYS B 29 13.545 50.606 25.960 ATOM 436 O LYS B 29 12.781 51.552 26.227 i.e. no B-values, no occupancies, no CRYST1 etc. Again, I am not sure this mutilation corresponds to the problem case you describe. Best, Tim
