Re: [PyMOL] code for calculating surface area

On Mon, 19 Jul 2004 18:27:18 +0930, Michael Sorich wrote: Hi, Could someone point me to the code used to calculate surface area (i.e. code to calculate surface dots and the code to find the area of the dots)? I presume that it is somewhere in the PyMOL\modules\pymol or PyMOL\modules\chempy m

[PyMOL] distance from plane

Hi Pymolers! Is there a way for me to define a plane of atoms say 4 Nitrogens in a heme complex and then determine how far out-of-plane the Fe atom is? If so either in Pymol or another program I'd love to know the secret. Thanks, Kristl kri...@physics.purdue.edu

Re: [PyMOL] distance from plane

Hi Kristl, I'm not sure if PyMOL can do it, but it's not too hard to do a bit of vector algebra which gives the answer. Let the coordinates of the nitrogens be A, B, C, D, and the iron atom F. Compute the centre of your nitrogens: X = (A + B + C + D) / 4 Then you work out a normal to the plan

[PyMOL] auto_zoom

I can't seem to turn off the auto_zoom feature. Whether I have turned it on or off, pymol always zooms in on a newly 'load'ed object. Is there any way to load a file without changing the view? Using get_view before loading the file and set_view after loading works, but it seems pretty clunky