<div dir="ltr">Hi Tristan and Tom, <div><br></div><div>Thanks very much! Very appreciated! I did play with ISOLDE with the mentioned guidance. I faced the same issues as mentioned by Tom. I thought I should try it a few more times and then reply. </div><div><br></div><div>So, I encountered this "at least one residue in your model does not match any templates in the MD forcefiled" warning first; and then it asked me to "addh". And then the same as Tom mentioned. The force I have is more of a "directional" force. I wonder is it possible to have a torque force? Or, is it possible to set a group of amino acids as one rigid body? </div><div><br></div><div>Very appreciate the fiddling (manual modeling) guidance too. </div><div><br></div><div>Roden</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Oct 25, 2021 at 10:02 PM Tom Goddard <<a href="mailto:goddard@sonic.net" target="_blank">goddard@sonic.net</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
Hi Roden, Tristan,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Tom<br>
<br>
<br>
<br>
<div>On 10/24/2021 1:49 AM, Tristan Croll
via ChimeraX-users wrote:<br>
</div>
<blockquote type="cite">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Hi Roden,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
This should be reasonably straightforward with the ISOLDE plugin
(<a href="https://urldefense.com/v3/__https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde__;!!Nmw4Hv0!jtJ8dNnTQ0tJc0CLw8HqKh7NIbLUHH72Nc6AJZpi2582f8VOx0v-FbJqs87FyKfCyVw$" id="gmail-m_891825142524022685gmail-m_-6323053964671548089LPNoLPOWALinkPreview" target="_blank">https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde</a>).
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:</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<ul>
<li><span>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.</span></li>
<li><span>Start ISOLDE. Then, assuming your protein is model
#1, do the following commands:</span></li>
<ul>
<li><span>isolde restrain distances #1 distanceCutoff 5 </span></li>
<li><span>isolde restrain torsions #1 angleRange 60</span></li>
<li>isolde sim start #1</li>
</ul>
<li>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@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.</li>
<li>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".</li>
<li>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.</li>
</ul>
<div>Happy modelling!</div>
<div><br>
</div>
<div>-- Tristan</div>
</div>
<br>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_891825142524022685gmail-m_-6323053964671548089divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b>
ChimeraX-users <a href="mailto:chimerax-users-bounces@cgl.ucsf.edu" target="_blank"><chimerax-users-bounces@cgl.ucsf.edu></a> on
behalf of Roden Deng Luo via ChimeraX-users
<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank"><chimerax-users@cgl.ucsf.edu></a><br>
<b>Sent:</b> 23 October 2021 16:30<br>
<b>To:</b> <a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>
<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank"><chimerax-users@cgl.ucsf.edu></a><br>
<b>Subject:</b> [chimerax-users] Refine predicted structure by
pulling</font>
<div> </div>
</div>
<div>
<div dir="ltr">Dear ChimeraX Users,<br>
<div><br>
</div>
<div>There is this AlphaFold prediction: <a href="https://urldefense.com/v3/__https://alphafold.ebi.ac.uk/entry/P02549__;!!Nmw4Hv0!jtJ8dNnTQ0tJc0CLw8HqKh7NIbLUHH72Nc6AJZpi2582f8VOx0v-FbJqs87FZ78SQ3E$" target="_blank">https://alphafold.ebi.ac.uk/entry/P02549</a>.
And we know this protein should be more or less in
a rod-like shape rather than a globular shape:
<a href="https://urldefense.com/v3/__https://en.wikipedia.org/wiki/Spectrin__;!!Nmw4Hv0!jtJ8dNnTQ0tJc0CLw8HqKh7NIbLUHH72Nc6AJZpi2582f8VOx0v-FbJqs87F7tqKeq8$" target="_blank">https://en.wikipedia.org/wiki/Spectrin</a>
and related literature such as
<a href="https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218374/__;!!Nmw4Hv0!jtJ8dNnTQ0tJc0CLw8HqKh7NIbLUHH72Nc6AJZpi2582f8VOx0v-FbJqs87FiXfOrTA$" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218374/</a>.
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? </div>
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>Best,</div>
<div>Roden</div>
</div>
<br>
<div>
<hr>
</div>
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</blockquote>
<br>
</div>
</blockquote></div>
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