pdbSurface
From EosPedia
pdbSurface is Eos's Command that gets Information of atom surface from PDB file.
Contents
List of option
Main option
| Option | Essential/Optional | Description | Default |
|---|---|---|---|
| -i | Essential | Input: PDB | NULL |
| -o | Essential | Output: PDB | NULL |
| -order | Optional | order: [A] | 1.7 |
| -refine | Optional | Refine: Meshsize = Order/Refine | 2 |
| -size | Optional | Refine: Shell thickness = Order/Refine*Size | 3 |
| -weight | Optional | weight | 100.0 |
| -mergin | Optional | SearchArea | 3.0 |
| -thres | Optional | threshold | 0.0 |
| -c | Optional | ConfigurationFile | NULL |
| -m | Optional | Mode | 0 |
| -h | Optional | Help |
-m details
| Value | Description |
|---|---|
| 0 |
Execution example
Input file image
 |
Gravity Centre(CA) Atom far from Centre(CA) |
6.053012e+00 2.519590e+01 1.189075e+01 3.286664e+01 |
Inputdata(part)
... ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00 14.06 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 17.27 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 16.41 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 16.12 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 17.94 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 19.41 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 21.82 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00 23.68 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 15.08 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 16.71 C ...
Case: Options only essential
Outputdata(part)
...
↓Items of Temperature Factor is changed.
ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N
ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 72.48 0 C
ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 3.60 0 C
ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 52.08 0 O
ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00100.00 0 C
ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00100.00 0 C
ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 21.50 0 S
ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C
ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.93 0 N
ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 3.23 0 C
...
Option -order
Case: order=1.9
... ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 24.74 0 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 1.05 0 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 8.75 0 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 34.92 0 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 0.12 0 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 5.53 0 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.12 0 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.00 0 C ...
Option -refine
Case: refine=1
... ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 17.24 0 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 16.69 0 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00100.00 0 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 32.91 0 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 9.69 0 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 68.76 0 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00 68.76 0 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 16.69 0 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 26.46 0 C ...
Option -size
Case: size=5
... ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00100.00 0 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 32.30 0 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 90.33 0 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00100.00 0 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00100.00 0 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 42.23 0 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 8.91 0 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 12.07 0 C ...
Option -mergin=2.8
Case: mergin=2.8
... ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00100.00 0 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 3.60 0 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 52.08 0 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00100.00 0 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00100.00 0 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 96.55 0 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 12.72 0 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.93 0 C ...
Option -thres
Case: thres=0.1
... ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 37.57 0 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 1.46 0 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 32.12 0 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 62.40 0 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 36.08 0 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 12.52 0 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.53 0 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.93 0 C ...
Option -weight
Case: weight=1000, thres=0.1
... ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 37.57 0 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 1.46 0 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 32.12 0 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 62.40 0 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 36.08 0 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 12.52 0 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.53 0 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.93 0 C ...
