[chimerax-users] Refine predicted structure by pulling
Roden Deng Luo
deng.luo at kaust.edu.sa
Tue Oct 26 04:00:01 PDT 2021
Dear Tristan,
Thanks! I think this is exactly what I have been looking forward to for
quite some time. A few follow-up questions.
1. What is your hardware and how long does it take to reach the state you
showed? I got one RTX 3090 on my local workstation (dual boot for Win10 and
Ubuntu). Additional four A6000 on a remote ubuntu server and V100s on a
cluster. Do you think I would need to bother with setting up the workflow
and X11 forwarding on the remote machines or one RTX 3090 is fine for daily
tasks?
2. I feel intimidated by the jargons mentioned above. I found this
documentation (https://isolde.cimr.cam.ac.uk/documentation/). Apart
from that, do you have other suggestions for reading materials?
3. Would it be possible to have multiple proteins in the scene and
incorporate chemical crosslink data? It gives us the information of amino
acid X should be within e.g. 30 Å to amino acid Y.
4. Would it be possible to constrain the structure inside a general mesh
(e.g. obj file) rather than an EM density map?
Thanks,
Roden
On Mon, Oct 25, 2021 at 11:37 PM Tristan Croll <tic20 at cam.ac.uk> wrote:
> Result of some quite aggressive stretching (alternating pulling on
> residues 2000 onwards and 1-700, extending the tugged selection at both
> ends as things straightened out). This was with my dev ISOLDE build
> allowing me to use the "adjustForConfidence true" argument and an 8
> Angstrom distance cutoff, which definitely helped keep things under control
> (also ended up restraining torsions with "isolde restrain torsions #1".
> Quick-and-dirty video overview of the final model at
> https://drive.google.com/file/d/15zCt7WF7W6rBLoujMhFwgdpDYaPsYMB-/view?usp=sharing
> <https://urldefense.com/v3/__https://drive.google.com/file/d/15zCt7WF7W6rBLoujMhFwgdpDYaPsYMB-/view?usp=sharing__;!!Nmw4Hv0!lCB3QYi96tlHwoqUxwqr0KVeJnh1_mPFwsjQ89mTgsUb6GWyfULSELF3pDkSS_JfJXg$>,
> showing that almost all the distance restraints remain well satisfied,
> except for a few at the hinges.
>
> Hope you find it useful!
>
> Tristan
>
> ------------------------------
> *From:* ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of
> Tristan Croll via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
> *Sent:* 25 October 2021 21:14
> *To:* goddard <goddard at sonic.net>; chimerax-users at cgl.ucsf.edu <
> chimerax-users at cgl.ucsf.edu>; Roden Deng Luo <deng.luo at kaust.edu.sa>
> *Subject:* Re: [chimerax-users] Refine predicted structure by pulling
>
> Hi Tom,
>
> Yes, "kappa" is the stiffness. Default in the current release is 5, (as
> specified in the documentation via "usage isolde restrain") which I agree
> is very soft for this particular purpose - after playing around with it a
> bit I find "isolde restrain distances #1 distance 5 kappa 100 fallOff -3"
> works quite well. The extra "adjustForConfidence true" argument coming in
> the new ISOLDE release (not yet available - here in a few weeks) will help
> further - because it uses AlphaFold's own confidence on residue-residue
> distances, it can extend the distance restraints over a longer range (e.g.
> the default 8 Angstroms) while ignoring spurious chance contacts between
> residues. Will play around a little more and share the result.
>
> -- Tristan
> ------------------------------
> *From:* Tom Goddard <goddard at sonic.net>
> *Sent:* 25 October 2021 20:01
> *To:* chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>; Roden
> Deng Luo <deng.luo at kaust.edu.sa>; Tristan Croll <tic20 at cam.ac.uk>
> *Subject:* Re: [chimerax-users] Refine predicted structure by pulling
>
> 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
> <https://urldefense.com/v3/__https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde__;!!Nmw4Hv0!lCB3QYi96tlHwoqUxwqr0KVeJnh1_mPFwsjQ89mTgsUb6GWyfULSELF3pDkS07ItNcc$>).
> 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>
> <chimerax-users-bounces at cgl.ucsf.edu> on behalf of Roden Deng Luo via
> ChimeraX-users <chimerax-users at cgl.ucsf.edu> <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>
> <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
> <https://urldefense.com/v3/__https://alphafold.ebi.ac.uk/entry/P02549__;!!Nmw4Hv0!lCB3QYi96tlHwoqUxwqr0KVeJnh1_mPFwsjQ89mTgsUb6GWyfULSELF3pDkS138lyq8$>.
> And we know this protein should be more or less in a rod-like shape rather
> than a globular shape: https://en.wikipedia.org/wiki/Spectrin
> <https://urldefense.com/v3/__https://en.wikipedia.org/wiki/Spectrin__;!!Nmw4Hv0!lCB3QYi96tlHwoqUxwqr0KVeJnh1_mPFwsjQ89mTgsUb6GWyfULSELF3pDkSPVkUGws$>
> and related literature such as
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218374/
> <https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218374/__;!!Nmw4Hv0!lCB3QYi96tlHwoqUxwqr0KVeJnh1_mPFwsjQ89mTgsUb6GWyfULSELF3pDkSkI3UiIc$>.
> 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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