[phenixbb] heavy atom in pdb for refinement

crystallogrphy qunwan1 at gmail.com
Fri Sep 11 14:49:51 PDT 2009


Hi,
I have Zn atoms in my pdb for refinement. However, it failed with the
following scripts. Do I have to create a libary of this heavy atom?
Number of atoms with unknown nonbonded energy type symbols: 6
    "ATOM      1 Zn    Zn Z   1 .*.    Zn  "
    "ATOM      2 Zn    Zn Z   2 .*.    Zn  "
    "ATOM      3 Zn    Zn Z   3 .*.    Zn  "
    "ATOM      4 Zn    Zn Z   4 .*.    Zn  "
    "ATOM      5 Zn    Zn Z   5 .*.    Zn  "
    "ATOM      6 Zn    Zn Z   6 .*.    Zn  "
  Time building chain proxies: 1.78, per 1000 atoms: 0.45

Here is the format of my pdb:
.....
ATOM      1 Zn    Zn Z   1      32.028  47.603  13.955  1.00 30.00
Zn
ATOM      2 Zn    Zn Z   2      29.017  71.434   8.164  1.00 30.00
Zn
ATOM      3 Zn    Zn Z   3      39.223  49.330  -6.810  1.00 30.00
Zn
ATOM      4 Zn    Zn Z   4      24.811  89.144  -4.406  1.00 30.00
Zn
ATOM      5 Zn    Zn Z   5      23.652  72.429   6.125  1.00 30.00
Zn
ATOM      6 Zn    Zn Z   6      30.132  63.054 -31.918  1.00 30.00
Zn
TER         7         Zn      6
ATOM     10 CL    CL L   1      20.125  63.405  10.719  1.00 30.00
CL
TER        11        CL       1
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