Hi,
off list we figured out that the occupancies (and B factors) were
missing in the pdb file (no occ-> no atoms-> no clashes).
I have fixed Coot as to permanently be able to add new b factor and occ
columns (available from revision 5077). Please use the functions
fill_occupancy_residue_range
set_b_factor_residue_range
BL
> 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/
>
> -----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
>
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