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:[log in to unmask]]
Sent: Mittwoch, 21. Mai 2014 14:54
To: [log in to unmask]; [log in to unmask]
Subject: Re: [ccp4bb] Minimum requirements for validation/coot/probe/
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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
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