Dan,
Yes, those files aren't really valid PDBs, but you can probably
solve this by assigning a distinct chain to the waters and rebuilding:
alter hoh/, chain='X'
sort
Cheers,
Warren
--
mailto:[email protected]
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf Of
> Daniel Rigden
> Sent: Friday, July 16, 2004 3:14 AM
> To: [email protected]
> Subject: [PyMOL] sequence viewer problem on some PDB files
>
> Hi
>
> It looks to me as if there is a glitch in the sequence viewer
> for some PDB files like 4PFK. The symptom is that waters get
> mixed up among the protein sequences as in the snapshot here
>
> http://pcwww.liv.ac.uk/~drigden/dross.png
>
> If you write the structure out again you get things like this
>
> ATOM 40 N GLY 5 20.601 -28.694 4.635 1.00
> 37.79
> 4PFK N
> ATOM 41 CA GLY 5 19.386 -28.380 5.423 1.00
> 41.21
> 4PFK C
> ATOM 42 C GLY 5 19.278 -26.841 5.426 1.00
> 42.59
> 4PFK C
> ATOM 43 O GLY 5 20.254 -26.164 5.038 1.00
> 43.67
> 4PFK O
> HETATM 44 O HOH 5 4.786 -19.354 8.074 1.00
> 34.51
> 4PFK O
> HETATM 45 O HOH 6 7.048 -4.823 8.185 1.00
> 20.29
> 4PFK O
> ATOM 46 N VAL 6 18.116 -26.349 5.824 1.00
> 38.63
> 4PFK N
> ATOM 47 CA VAL 6 17.842 -24.904 5.901 1.00
> 33.77
> 4PFK C
> ATOM 48 C VAL 6 16.826 -24.721 7.009 1.00
> 35.07
> 4PFK C
> ATOM 49 O VAL 6 15.935 -25.593 7.057 1.00
> 37.40
> 4PFK O
> ATOM 50 CB VAL 6 17.427 -24.327 4.537 1.00
> 31.75
> 4PFK C
> ATOM 51 CG1 VAL 6 16.199 -24.987 3.908 1.00
> 28.52
> 4PFK C
> ATOM 52 CG2 VAL 6 17.323 -22.819 4.592 1.00
> 25.99
> 4PFK C
> TER 53 VAL 6
> HETATM 54 O HOH 7 7.246 -12.026 8.967 1.00
> 16.51
> 4PFK O
> ATOM 55 N LEU 7 16.985 -23.701 7.817 1.00
> 35.71
> 4PFK N
> ATOM 56 CA LEU 7 16.018 -23.467 8.906 1.00
> 38.35
> 4PFK C
>
> After playing a bit it seems as if it applies particularly to
> old, non-standard PDB files where
>
> a) Protein and HETATMs have the same chain ID (in the case of
> 4pfk, chain ID is blank for both)
> b) Water numbering overlaps protein residue numbering
>
> Wish I'd noticed this one yesterday too...
>
> Cheers
>
> Dan
>
>
> --
> Dr Daniel John Rigden Tel:(+44) 151 795 4467
> School of Biological Sciences FAX:(+44) 151 795 4414
> Room 101, Biosciences Building
> University of Liverpool
> Crown St.,
> Liverpool L69 7ZB, U.K.
>
>
>
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