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#73 select by chain in the menu

v10
closed
Nicolas
5
2006-09-18
2005-10-16
Angel Herraez
No

The pop-up menu allows to color by chain.
It would be interesting --for the naive user, not the
command line-- to be able to select a chain in the
model, similarly to existing select by model, by
residue name, by element...
angel.herraez@uah.es

Discussion

  • Nicolas
    Nicolas
    2006-03-26

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    I started looking at this and I have questions :

    - simple one: what is the script command to select a chain ?

    - for other developers: how do I get access to the list of
    chains through the JmolViewer API ?

    - functional: how should the list be displayed, especially
    for a multi-model file ? :
    * with sub-menu for each model ?
    * everything at the same level, but then how do you deal
    with a chain ID that exists in several models ? display it
    for each model (with a label like <Model>-<ChainID>),
    display it once so that it selects the chain is each model, ...

     
  • Angel Herraez
    Angel Herraez
    2006-03-26

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    To select chain "a", the script is
    select *:a
    (Chain ID's can be a to z, A to Z, 1 to n; may be
    case-sensitive depending on the setting of "set
    ChainCaseSensitive")

    I would not expect to have a choice depending on models; I
    don't think there is one when selecting by residue name or
    element name. So, selecting chain A would select that chain
    in all models. A list of available chains would be enough,
    as one gets when choosing "Select > Protein > Residue name".

     
  • Nicolas
    Nicolas
    2006-04-30

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    Angel, could you point me to a data files for testing this
    feature ?
    I'd like file(s) with:
    - multiple models,
    - some chain ID existing in one model
    - some chain ID existing in several models

     
  • Angel Herraez
    Angel Herraez
    2006-04-30

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    user_id=1065324

    1gzx.pdb : 1 model, several chains (4 protein chains,
    including hetero ligands, and 4 water "chains")

    1ch1.pdb : 1 model, 1 chain, labeled 'A'

    1myf.pdb: 12 models, 1 chain, no chain ID

    1hls.pdb : 20 models, 2 chains A and B

     
  • Bob Hanson
    Bob Hanson
    2006-08-22

    • status: open --> closed
     
  • Bob Hanson
    Bob Hanson
    2006-08-22

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    set picking chain

     
  • Nicolas
    Nicolas
    2006-08-23

    • assigned_to: nobody --> nicove
    • status: closed --> open
     
  • Bob Hanson
    Bob Hanson
    2006-09-18

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    user_id=1082841

    done

     
  • Bob Hanson
    Bob Hanson
    2006-09-18

    • status: open --> closed