Hi Roden, Tristan,

  I tried Tristan's suggestion for straightening the long AlphaFold helix model.  It didn't work well for me because the restraints were too soft, so if I pulled on the first 160 residues it hardly moved the attached 2000 and instead just distorted the linker.  Tristan is there a way to make the restraints much stiffer?  I see the "isolde restrain distance" command has a "kappa" option and "falloff" option but I don't know if kappa is a stiffness or what magnitude it usually uses.

  I think a better approach is to just rigidly rotate and translate large straight sections by hand using the "Move atoms" mouse mode in the ChimeraX 1.3 toolbar tab called Right Mouse.  I tried this and have attached an image of about 10 minutes fiddling by hand.  I hover the mouse at a hinge residue to get the residue number and then select everything on one side of that hinge "select :1182-2419" then use the right mouse button in the "move atoms" mode, holding the shift key down to do rotations, and no shift key to do translations.  I zoom in on the hinge to try to adjust so the bond is not stretched and to avoid clashes.  It would probably take 1 hour to do a good job.  With my 10 minute test I then saved an mmCIF file and tried in ChimeraX 1.2.5 to minimize it with ISOLDE, but it said there were severe clashes.

    Tom



On 10/24/2021 1:49 AM, Tristan Croll via ChimeraX-users wrote:
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:

Happy modelling!

-- Tristan

From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Roden Deng Luo via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: 23 October 2021 16:30
To: chimerax-users@cgl.ucsf.edu <chimerax-users@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

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