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 [EMAIL PROTECTED] ::telephone: +44 (0) 1223 494629
