Colorize a protein



  • After loading a structure, if i choose to colore it by secondary structure (ss), the whole protein is green. I've to select Secondary structure representation then ss color to see amino acids color by ss. And colors are not the same between ss representation and ss residues colors...not good !
    If i choose a surface representation, it take previously selected colors. If i want to change the color, i have to create another surface, correct ?
    In the surface properties, if i change the Opacity from 100% to 99% (or less), the surface disappear.
    For a selected residue with hydrophobic color, if i change the hydrophobic scale, nothing change with the color of the residue....



  • Dear @Emmanuel ,

    Thank you for your feedback!

    if i choose to colore it by secondary structure (ss), the whole protein is green. I've to select Secondary structure representation then ss color to see amino acids color by ss.

    Sorry for the issue. This has been fixed in the upcoming release of SAMSON.

    And colors are not the same between ss representation and ss residues colors...

    By default, the secondary structure representation is colorized based on the residue sequence number. You can easily colorize the secondary structure visual model into any color scheme you like by applying it to the visual model.

    If i choose a surface representation, it take previously selected colors. If i want to change the color, i have to create another surface, correct ?

    It applies the color of the structure to which the surface was applied. If you want to change the color you may update the surface or generate another one.

    In the surface properties, if i change the Opacity from 100% to 99% (or less), the surface disappear.

    Thank you for reporting it, we will check it.

    For a selected residue with hydrophobic color, if i change the hydrophobic scale, nothing change with the color of the residue....

    If you modify the hydrophobicity scale only for a few residues in the whole structure would you expect these residues to be recolored? In the case, when one part of residues have one hydrophobicity scale, while another part of residues has another hydrophobicity scale, the colorization won't have much sense since hydrophobicity scales are different. This is why we don't automatically update the colorization. But you can update it yourself by applying again the colorization by the hydrophobicity of the whole structure or only its part.



  • If i change the hydrophobic scale for the whole residues, i expect to see residues be recolored but nothing append. I didn't find an update button in the inspector



  • @emmanuel
    For now, you can just reapply the Hydrophobicity color scheme (Biology menu > Colorize > Hydrophobicity).


Log in to reply
 

Looks like your connection to SAMSON Connect - Forum was lost, please wait while we try to reconnect.