pdb2SketchMacro
From EosPedia
pdb2SketchMacro is Eos's Command.
Contents
List of option
Main option
| Option | Essential/Optional | Description | Default |
|---|---|---|---|
| -i | Optional | Input: PDB | stdin |
| -o | Optional | Output: ASCII | stdout |
| -MolName | Optional | Molecule Name (recommend 2 words or less) | TS |
| -c | Optional | ConfigurationFile | NULL |
| -m | Optional | Mode | 15 |
| -h | Optional | Help |
-m details
| Value | Description |
|---|---|
| 1 | Helix sketched with spirals |
| 2 | Sheet sketched with arrows |
| 4 | Turn sketched with rattler |
| 8 | No structure sketched with rattler |
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 |
Example of options only essential
sam_atom_in Input.pdb TS sketch_object TSH_A1 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone TS A16 A25 red sketch_add TS A16 A25 end_object sketch_object TSH_A2 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone TS A65 A74 red sketch_add TS A65 A74 end_object sketch_object TSH_A3 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone TS A87 A103 red sketch_add TS A87 A103 end_object sketch_object TSH_A4 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone TS A127 A137 red sketch_add TS A127 A137 end_object sketch_object TSH_A5 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone TS A152 A164 red sketch_add TS A152 A164 end_object sketch_object TSS__S sketch_setup Arrow solid 2.5 0.5 3.75 2 7 3 2 sketch_type Arrow paint_zone TS A37 A46 blue sketch_add TS A37 A46 paint_zone TS A49 A58 blue sketch_add TS A49 A58 paint_zone TS A2 A9 blue sketch_add TS A2 A9 paint_zone TS A77 A83 blue sketch_add TS A77 A83 paint_zone TS A111 A116 blue sketch_add TS A111 A116 paint_zone TS A141 A143 blue sketch_add TS A141 A143 end_oject sketch_object TSN__1 sketch_setup Rattler solid 0.5 7 2 sketch_type Rattler paint_zone TS A1 A2 white sketch_add TS A1 A2 end_object sketch_object TSN__2 sketch_setup Rattler solid 0.5 7 2 sketch_type Rattler paint_zone TS A9 A16 white sketch_add TS A9 A16 end_object ... sketch_object TSN_11 sketch_setup Rattler solid 0.5 7 2 sketch_type Rattler paint_zone TS A143 A152 white sketch_add TS A143 A152 end_object sketch_object TSN_12 sketch_setup Rattler solid 0.5 7 2 sketch_type Rattler paint_zone TS A164 0 white sketch_add TS A164 0 end_object
Option -m
Case: m=1
sam_atom_in Input.pdb TS sketch_object TSH_A1 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone TS A16 A25 red sketch_add TS A16 A25 end_object sketch_object TSH_A2 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone TS A65 A74 red sketch_add TS A65 A74 end_object sketch_object TSH_A3 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone TS A87 A103 red sketch_add TS A87 A103 end_object sketch_object TSH_A4 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone TS A127 A137 red sketch_add TS A127 A137 end_object sketch_object TSH_A5 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone TS A152 A164 red sketch_add TS A152 A164 end_object
Case: m=8
sam_atom_in Input.pdb TS sketch_object TSN__1 sketch_setup Rattler solid 0.5 7 2 sketch_type Rattler paint_zone TS A1 A2 white sketch_add TS A1 A2 end_object sketch_object TSN__2 sketch_setup Rattler solid 0.5 7 2 sketch_type Rattler paint_zone TS A9 A16 white sketch_add TS A9 A16 end_object ... sketch_object TSN_11 sketch_setup Rattler solid 0.5 7 2 sketch_type Rattler paint_zone TS A143 A152 white sketch_add TS A143 A152 end_object sketch_object TSN_12 sketch_setup Rattler solid 0.5 7 2 sketch_type Rattler paint_zone TS A164 0 white sketch_add TS A164 0 end_object
Option -MolName
Case: MolName=XX, m=1
Input.pdb XX sketch_object XXH_A1 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone XX A16 A25 red sketch_add XX A16 A25 end_object sketch_object XXH_A2 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone XX A65 A74 red sketch_add XX A65 A74 end_object sketch_object XXH_A3 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone XX A87 A103 red sketch_add XX A87 A103 end_object sketch_object XXH_A4 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone XX A127 A137 red sketch_add XX A127 A137 end_object sketch_object XXH_A5 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone XX A152 A164 red sketch_add XX A152 A164 end_object
