#128 chain/hetero/model list variables

open
Bob Hanson
None
5
2010-11-22
2007-11-01
Rolf Huehne
No

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:

chain_list
hetero_list
model_list

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

Discussion

  • Bob Hanson
    Bob Hanson
    2007-11-09

    Logged In: YES
    user_id=1082841
    Originator: NO

    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

    Logged In: YES
    user_id=1344570
    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);
    spacefill;
    select siteprev;
    color cpk;

     
  • Nicolas
    Nicolas
    2010-11-22

    • assigned_to: nobody --> hansonr