-----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 On 05/21/2014 01:43 PM, Bernhard Rupp wrote: > Dear All, > > > > I experienced an odd observation with some philosophical > consequences (here we go again) > > > > When I run a model obtained from a perhaps popular but until > further examination unnamed server, > > and validate through coot/validate, the model kills probe/reduce > which normally works great. > > > > Following observations: > > Normally, 3 windows appear: Generic objects, Flips, Molprobity > Probe clash gaps; and the H-added model and the little dots and > spikes are displayed. > > For that model I get only the Flips window with 'no adjustment', > and an empty Molprobity Probe Clash Gaps Window. > > > > The model has only a CRYST1 record, > > does NOT contain a B factor or occupancy column > > it HAS a TER record. > > > > OK, I probably can paste/awk those missing columns in there with > fake values. > > > > But now the consequences: > > > > Also the PDB adit server rejects that model, although I cannot see > why one should not be able to do at least a geometry > > validation with coordinates alone. > > > > Particularly the sucker models returned from structural > bioinformatics servers (which understandably and in rare humbleness > > > do not contain occs or Bs), need exactly this validation the most. > The model in question has overlapping backbone sections and rmszs > >70. > > > > What means are left for a user to validate such stuff? If the PDB > wants to be a true structure resource for users, it should allow > such > > minimum validation of any coordinate model, and not reject > everything that does not fit stringent deposition criteria. I do > not need > > CRYST or TER records and not even B's or Occs if I want to know if > a model is really bad. I think that these weird models > > that are spit out by certain bioinformatics servers are a lot more > hazardous to an innocent user than a poor experimental model. > > > > Cheers, BR > > > > ----------------------------------------- Trigger warning > --------------------------------------------------- > > This message may or may not contain references to issues of > privilege and oppression > > including but not limited to enantiophobia, point classism, > heteroatomism, transbondism, > > cisbonding, sizeism, curvature, references to color, alcohol, > blood, small insects, disgusting cells, and > > any combination thereof that may cause symptoms ranging from > discomfort and anxiety to violent > > physical response in sensitive individuals and must therefore be > labeled as potentially > > hazardous to your comfort and well-being. > > > > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTfKH6UxlJ7aRr7hoRAq56AKD03HICPNfcDlTGVyQvoQuasGUtHwCfdRLa ZbOuyXr5Yylh6OyTLbz8ftE= =SdJM -----END PGP SIGNATURE-----
