Solvent Accessible Surface Visualization - surface properties?



  • Hello!

    I have been using the built-in visualization "Solvent Accessible Surface" to create surfaces on proteins imported from pdb. I was wondering if it was possible to access some of the properties of the created surface, such as which molecules are included in it, their relative exposed surface area, etc.

    I also saw that you can change the radius of the probe, up to 3A. Is there a way to increase this probe radius, e.g. up to 20A?

    Thank you for your help!



  • Dear @Matthew-1 ,

    Currently, for the Solvent Accessible Surface visual model, it is not possible to access the list of nodes (molecules, atoms, etc) to which it is applied to. We can expose this in the next version along with increasing the maximum value of the probe radius.

    If you want to compute the Solvent Accessible Surface Area (SASA) of a molecule, then you can use the Protein-Ligand Interaction Analyzer: just set the molecule as a receptor, do not set any ligand, specify the probe radius for SASA computations (you can set up to 30A) and click Analyze - it will compute SASA for the receptor along with some other properties. Please note, that setting a large value for the probe radius will lead to more computations due to the used algorithm.



  • Thank you for your quick response, it is much appreciated!


Log in to reply
 

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