#128 chain/hetero/model list variables

Rolf Huehne

The "site_list" variable introduced in 11.3.33 is very useful.

It would be very useful for structure dependent scripting if similar lists were available for chains, hetero components and models:


In the case of hetero components it would also help if the corresponding full names were available additionally (if provided in the file).


  • Bob Hanson

    Bob Hanson - 2007-11-09

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    Interesting. What would you like these to be like when you have multiple models and maybe even something like:

    1.1 [pdb file 1 model 1]
    2.1 [pdb file 2 model 1]
    2.2 [pdb file 2 model 2]
    2.3 [pdb file 2 model 3]
    3.1 [a ligand]
    4.1-4.6 [an animated xyz file]

    Would the chain list somehow associate chains with specific models?
    Same question for HET.

  • Rolf Huehne

    Rolf Huehne - 2007-11-10

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    Originator: YES

    I'm not used yet to loading totally different models at the same time.
    The "site_list" which is already available has of course the same problem.

    There are 2 important aspects here that might contradict each other:

    1) usability of the information directly within Jmol scripts (e.g. for automatic batch processing with the application)

    2) compatibility with complex multiple file cases as described

    I would expect that these complicated cases will be the exception and might require javascript aid anyhow. So it might be sufficient to have simple lists without file/model specification within Jmol and some kind of "getProperty" request to obtain the full information.

    I use the "site_list" for example in an automatic image generation script to set a specific rendering of active sites:

    select none;
    for (var i=1; i<=site_list.size; i=i+1);
    script inline "select selected OR " + site_list[i];
    end for;
    define siteprev selected;
    wireframe 100;
    select selected and (not bonded or ligand);
    select siteprev;
    color cpk;

  • Nicolas

    Nicolas - 2010-11-22
    • assigned_to: nobody --> hansonr

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