Changing the membrane Thickness (THKN)

[Anonymous]

Hello (Py)Rosetta community

Currently whenever I add a membrane to my pose the membrane thickness is always 15 A (30 total). I would like to elongate that in order to model different types of phospholipids found in bacterial cells.

My best idea to do this is to change the x-coordinate of the membrane residue in the pose object, using the following commands

>>> AID = AtomID(1, pose.size())

>>> pose.set_xyz(AID, XYZ(30,0,0))

where XYZ is the function/method to create a rosetta.numeric.xyzVector object. It seems to successfully change the membrane info from 15 A to 30 A, but the score function scores it exactly the same is it did when it was 15 A, indicating that the change was only cosmetic.

Can anyone tell me who to change the membrane thickness? (such that it registers a different score).

Thank you in advance!

-Joel

[Anonymous]

Hello,

I am currently working on a new implicit membrane model with parameters for different lipid compositions. That should be coming to master within the next month or so. In the meantime, you can change the lipid composition in RosettaMP using the flag -mp:thickness. You can set this from pyrosetta by passing the flag “extra_options=-mp:thickness XX” where XX is your desired half thickness (e.g. 12 for a 24A membrane) in the init() function.

Rebecca

 

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