[chimerax-users] Refine predicted structure by pulling

[Tristan Croll]

Hi Roden,

This should be reasonably straightforward with the ISOLDE plugin (https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde). You'll also want to be working on a machine with a good GPU to make it feasible for a model this size. It'll be easier still with the new release coming in a few weeks, which has some added tools specifically for working with AlphaFold models. But with care you could do it now:


  *   first, check carefully for entanglement between distant domains (this is an issue for AlphaFold with these very long, flexible proteins - if distant parts of the protein have no coevolutionary signal they don't really "know" about each other and can end up trying to occupy the same space). Looks like your particular example is free of that problem.
  *   Start ISOLDE. Then, assuming your protein is model #1, do the following commands:
     *   isolde restrain distances #1 distanceCutoff 5
     *   isolde restrain torsions #1 angleRange 60
     *   isolde sim start #1
  *   Then, you'll want to use the "tug selection" mouse mode (third from bottom right of the ISOLDE panel). Make a selection for a suitable region to tug (e.g. "sel #1-100 at CA" to tug the N-terminus), and tugging forces applied by right-click-and-drag will be spread over that selection. Keep a close eye on the distance restraints - if they start to become too strained (lots of purple appearing), stop tugging and let the model settle.
  *   If you have unwanted distance restraints between domains that should be distant from each other, you can selectively release restraints on selected atoms with "isolde release distances sel".
  *   You might find it easier for a job like this to reduce the view to a C-alpha trace - just "hide ~@CA" - if you do this after you've started a simulation, it'll automatically revert to the all-atom view once you stop.

Happy modelling!

-- Tristan

________________________________
From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of Roden Deng Luo via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
Sent: 23 October 2021 16:30
To: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: [chimerax-users] Refine predicted structure by pulling

Dear ChimeraX Users,

There is this AlphaFold prediction: https://alphafold.ebi.ac.uk/entry/P02549. And we know this protein should be more or less in a rod-like shape rather than a globular shape: https://en.wikipedia.org/wiki/Spectrin and related literature such as https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218374/. I wonder is there a way that we can pull the two ends of the predicted structure while maintaining the secondary structures, mostly alpha-helices in this case, inside ChimeraX?

I am quite new to ChimeraX. I understand this is more fitted to an MD simulation. But I got to know there are options to fit a PDB to a density map. So I wondered if this can be achieved in ChimeraX.

Best,
Roden

________________________________
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211024/eaf812f9/attachment.html>