File: rename.tex
Last modified: 19-OCT-91



         ATOM  string
         RESIDUE  string
         SEGMENT  string
         CHAIN    char
         SEQUENCE string
         AUTOMATI  [inte]
         BACKWARD  [inte]

The atomic character data (ATOM, RESIDUE, SEGMENT names and SEQUENCE IDs) of the SELECTED atoms can be modified using the RENAME command sentence. This can save a lot of effort required to transfer the atomic coordinate files between different programs. The time consuming editor use can be avoided.

The INSERT/DELETE and APPEND/REMOVE are operating only on SEQUENCE names. APPEND appends a character after the current sequence names,


... SELECT ... END

The standard selection subcommand.


... ATOM string

RENAMES the selected atoms to something. (CD1 to CD).

> rena sele atom  name CD1 .a resi name ILE  end atom CD


... RESIDUE string

RENAMES the selected RESIDUE names tosomething. (SOL to H20).

> rena sele resi name SOL  end resi H2O


... SEGMENT string

RENAMES the selected SEGMENTs to something. (SOL to WAT).

> rena sele segm name SOL  end segm WAT



RENAMES chain identifiers of the given selection. In a combination with AUTO flag only the first found chain gets the given character, each following chain gets also the following characters from the ASCII table.

> rename chain A sele segm name MOL1 end

> show chain

See also "MAKE CHAIN" commad in make.html.


... SEQUENCE string

If no additional command wrod follows then the whole selection obtains the new sequence ID, otherwise the string following the SEQUENCE keyword is used as a root (APPEND, INSERT, AUTOMATI, BACKWARD) or not considered at all (DELETE, REMOVE).

> rename sele resi numb 4 end seq A4
> rename sele active end seq A auto
> rename sele active end seq A append


APPENDs the specified SEQUENCE character after the current sequence IDs.


REMOVES the last character from the sequence names.


Inserts the specified SEQUENCE character before the current SEQUENCE id string.


Deletes the first character of the sequence names.


... AUTOMATI [int]

Each additional residue will obtain the sequence ID root plus the current counter. The default start is 1.



> rename select atom name CD1 .and. residue name ILE end atom CD

> rename select residue number 1 end sequence -2

> rename sequence 33A select residue number 33 end

> rename select segment numb 1 end sequence A insert
> rename select segment numb 2 end sequence B insert

> rename select inhibitor end sequence I append

> rename sequence 33A select residue number 33 end

This rename will change the sequence IDs of a selection so that each seq ID starts with B and a consecutive number from 1 to nn is appended to it. (AUTOGENERATE)

> rename select active end seq B auto

Give new segment name to the specified selecttion of atoms. Be aware that the selection should contain complete residues, otherwise the command will not behave as you expect.

> rename sele active end segm MOLA