PyMOL plugin cannot load more than 10,000 SFAs (supportive fake atoms)

[Robert Welch]

If you try and load system with more than this number of faces/elements/nodes, it will only load a subset of them. This can make it difficult to change the vdw parameters of big, complex static objects such as microtubules. As a temporary fix, I would recommend creating vdw interactions via pins instead, using FFEA_pin_to_vdw. In the long-term this may not get fixed and we may simply migrate away from pymol instead, but I’m listing it here in case others run into it.

[Robert Welch]

More detailed instructions:

1. Open object in FFEA viewer with ‘load atoms’ set to ‘onto nodes’
2. Note down nodes near where you want to change the VDW parameters
3. Create pinfiles in python by creating an instance of FFEA_pin and add calling pin_radially
4. Apply the pinfiles for different vdw types using FFEA_pin_to_vdw

There is a command-line tool to make pins but it can’t add to pins (it just replaces the pinfile) so it’s probably better to make the pins in python, I added a feature that stops you from wiping the pin each time, just call FFEA_pin.pin_radially() with reset=1 (look, whoever wrote this had a vendetta against booleans and I decided not to mess with the idiom)

Rob

PS: i will not provide any more information, it’s a rope to hang you with, I won’t do it