I would like to calculate 3D-PSA by summing the contribution of polar atoms to the van der Waals molecular surface area. Is there a way to save a text file with the atomic contributions? I am having a hard time figuring out which value goes with which atom in the viewer window.
you should use the vdwsa surface calculator function of cxcalc that has a -i option, which lists the atomic increments in the order of the atoms.
cxcalc vdwsa -i oxa.mrv
gives the output:
id Van der Waals surface area (3D) increments
1 198,40 4,35;4,20;4,19;4,25;4,73;4,72;4,34;4,25;13,84;9,79;9,79;10,90;10,97;10,87;10,87;10,97;10,90;10,84;10,84;
More custom-made solution can be given by using the plugin API.
Can you give us the use-case or workflow so that we can give maybe a better solution?