Define new chain#
Defining a new chain by grouping a selection of atoms.
The function molsysmt.build.define_new_chain() allows you to group any set of atoms into a new chain. This is useful when working with merged or modified systems where chain identity needs to be explicitly reassigned.
Added in version 1.0.0.
How this method works#
API documentation
Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function:molsysmt.build.define_new_chain().
This function modifies the topology of the molecular system by assigning a new chain_id and chain_name to the selected atoms. The reassigned chain appears as an additional entry in the system’s chain list, without altering other chain definitions.
We begin by loading a protein structure from the PDB with ID 1TCD.
import molsysmt as msm
molsys = msm.convert('1TCD')
Let’s inspect the current chain composition of the system.
We now assign all water molecules to a new chain labeled 'C'.
This does not alter the identity of existing chains but adds a new one for the selected atoms.
msm.info(molsys, element='chain')
| index | id | name | n atoms | n groups | n components | molecule index | molecule type | entity index | entity name |
|---|---|---|---|---|---|---|---|---|---|
| 0 | 0 | A | 1906 | 248 | 1 | 0 | protein | 0 | TRIOSEPHOSPHATE ISOMERASE |
| 1 | 1 | B | 1912 | 249 | 1 | 1 | protein | 0 | TRIOSEPHOSPHATE ISOMERASE |
| 2 | 2 | A | 73 | 73 | 73 | [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74] | ['water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water'] | 1 | water |
| 3 | 3 | B | 92 | 92 | 92 | [75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166] | ['water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water'] | 1 | water |
Let’s confirm that the water molecules have been grouped into a new chain.
msm.build.define_new_chain(molsys, selection='molecule_type=="water"', chain_name='C')
msm.info(molsys, element='chain')
| index | id | name | n atoms | n groups | n components | molecule index | molecule type | entity index | entity name |
|---|---|---|---|---|---|---|---|---|---|
| 0 | 0 | A | 1906 | 248 | 1 | 0 | protein | 0 | TRIOSEPHOSPHATE ISOMERASE |
| 1 | 1 | B | 1912 | 249 | 1 | 1 | protein | 0 | TRIOSEPHOSPHATE ISOMERASE |
| 2 | 2 | C | 165 | 165 | 165 | [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166] | ['water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water'] | 1 | water |
This method is particularly useful when preparing systems for simulation, merging fragments, or when chain identity needs to be redefined after structural modifications.
See also
User guide > Tools > Basic > Info:
Display a summary of the system, including its chains.
User guide > Tools > Build > Merge:
Combine multiple molecular systems, which may require redefining chains.
User guide > Tools > Build > Add:
Add elements from one molecular system into another.
User guide > Tools > Basic > Set:
Change attribute values such as chain_name or chain_id.