sorry forgot
if the atom records have either GLU or ASP CO2 protonated
protonation over-rides torsional angles on renaming
kim
On Sat, 11 Aug 2007, Kim Henrick wrote:
> from www.ebi.ac.uk/~henrick/newpdb/
> get checknames.f
> standard_geometry.cif
>
>
>
> setenv STANDATA standard_geometry.cif
> f77 checknames.f -o checknames
>
> ./checknames
> running with no arguments gives the help info
> expects a file pdbxxxx.ent to be a normal pdb file
>
> (I am supposed to make this in Eleanor style
> by allow any input file but currently just pdb style
> file name entering just the idcode - '4tst' is
> not used in pdb for obvious phonetic reasons - maybe soon)
>
>
> making a mini pdb on your coordinates
>
>
> more pdb4tst.ent
> ATOM 55 N GLU A 15 -59.930 -39.249 -9.123 1.00 30.10 N
> ATOM 56 CA GLU A 15 -60.573 -38.776 -7.889 1.00 30.54 C
> ATOM 57 CB GLU A 15 -61.533 -37.599 -8.146 1.00 31.08 C
> ATOM 58 CG GLU A 15 -61.014 -36.528 -9.124 1.00 35.70 C
> ATOM 59 CD GLU A 15 -61.459 -36.784 -10.589 1.00 40.21 C
> ATOM 60 OE1 GLU A 15 -60.561 -36.946 -11.467 1.00 40.16 O
> ATOM 61 OE2 GLU A 15 -62.701 -36.815 -10.851 1.00 41.17 O
> ATOM 62 C GLU A 15 -61.334 -39.901 -7.182 1.00 29.34 C
> ATOM 63 O GLU A 15 -61.335 -39.989 -5.947 1.00 29.37 O
> TER
> END
>
> then run
>
> ./checknames 4tst
> Swapping OE1 OE2 for GLU A 15
> diff -bw pdb4tst.ent pdb4tst.rename
> 1,10c1,10
> < ATOM 55 N GLU A 15 -59.930 -39.249 -9.123 1.00 30.10 N
> < ATOM 56 CA GLU A 15 -60.573 -38.776 -7.889 1.00 30.54 C
> < ATOM 57 CB GLU A 15 -61.533 -37.599 -8.146 1.00 31.08 C
> < ATOM 58 CG GLU A 15 -61.014 -36.528 -9.124 1.00 35.70 C
> < ATOM 59 CD GLU A 15 -61.459 -36.784 -10.589 1.00 40.21 C
> < ATOM 60 OE1 GLU A 15 -60.561 -36.946 -11.467 1.00 40.16 O
> < ATOM 61 OE2 GLU A 15 -62.701 -36.815 -10.851 1.00 41.17 O
> < ATOM 62 C GLU A 15 -61.334 -39.901 -7.182 1.00 29.34 C
> < ATOM 63 O GLU A 15 -61.335 -39.989 -5.947 1.00 29.37 O
> < TER
> ---
>> ATOM 1 N GLU A 15 -59.930 -39.249 -9.123 1.00 30.10
> N
>> ATOM 2 CA GLU A 15 -60.573 -38.776 -7.889 1.00 30.54
> C
>> ATOM 3 C GLU A 15 -61.334 -39.901 -7.182 1.00 29.34
> C
>> ATOM 4 O GLU A 15 -61.335 -39.989 -5.947 1.00 29.37
> O
>> ATOM 5 CB GLU A 15 -61.533 -37.599 -8.146 1.00 31.08
> C
>> ATOM 6 CG GLU A 15 -61.014 -36.528 -9.124 1.00 35.70
> C
>> ATOM 7 CD GLU A 15 -61.459 -36.784 -10.589 1.00 40.21
> C
>> ATOM 8 OE1 GLU A 15 -62.701 -36.815 -10.851 1.00 40.16
> O
>> ATOM 9 OE2 GLU A 15 -60.561 -36.946 -11.467 1.00 41.17
> O
>> TER 10 GLU
>
>
>
>
>
--
Kim HENRICK [log in to unmask] ::telephone: +44 (0) 1223 494629
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