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Thanks again Tom.</div>
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The buried surface area was 1535 angstroms squared. Is that a "good" value? Also is that value calculated across the two proteins? There appears to be specific regions of the two proteins that are in contact. Is it possible to measure the buried area just
for those two regions.</div>
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A note on these two proteins. Both have specific structured regions (that are interacting) but also have disordered regions elsewhere that account for >50% of the proteins distances. I have looked at those regions using IUPred3.</div>
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Phil</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Tuesday, October 4, 2022 12:23 PM<br>
<b>To:</b> McClean, Phillip <phillip.mcclean@ndsu.edu><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] alphafold contacts output file</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Philip,
<div class=""><br class="">
</div>
<div class=""> The alphafold contacts code as it is currently written finds the pairs of close residues but does not remember which atoms were the closest so it can't easily output the closest atoms between a pair of residues. But the ChimeraX contacts command
or tool is actually intended to find contacting residues and uses more sophisticated criteria that take into account the van der Waals radii of the atoms.</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span><a href="https://www.cgl.ucsf.edu/chimerax/docs/user/tools/clashes.html" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/tools/clashes.html</a></div>
<div class=""> <a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html</a></div>
<div class=""><br class="">
<div> Confidence in whether two proteins really make a biological contact in for example a crystal structure where the proteins may must be touching due to crystal packing is usually judge by the total area of contact residues, not by how close individual
residues are to each other. The ChimeraX buried surface area calculation calculates how much surface is in contact (square Angstroms).</div>
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</div>
<div><span class="x_Apple-tab-span" style="white-space:pre"></span>measure buriedarea /A with /B</div>
<div><span class="x_Apple-tab-span" style="white-space:pre"></span>> Buried area between /A and /B = 484.71</div>
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<div> To judge if an AlphaFold prediction of a protein-protein interface is correct I suggest looking at both the buried surface area and also the the AlphaFold PAE values between residue pairs at the interface.</div>
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<div><span class="x_Apple-tab-span" style="white-space:pre"></span>Tom</div>
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<div><br class="">
<blockquote type="cite" class="">
<div class="">On Oct 4, 2022, at 10:08 AM, McClean, Phillip <<a href="mailto:phillip.mcclean@ndsu.edu" class="">phillip.mcclean@ndsu.edu</a>> wrote:</div>
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<span class="x_elementToProof x_ContentPasted0" style="font-size:12pt; margin:0px">Hi Tom,</span>
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<div class="x_elementToProof x_ContentPasted0" style="font-size:12pt; margin:0px">
Thanks. Found it on the desktop.</div>
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<div class="x_elementToProof" style="font-size:12pt; margin:0px"><span class="x_ContentPasted0" style="margin:0px">A follow-up Chimerax question (hopefully it shouldn't be a different thread). Is it possible to list the atoms that are in close contact in the
output file.</span><br class="x_ContentPasted0">
</div>
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</span></div>
<div class="x_elementToProof" style="font-size:12pt; margin:0px"><span class="x_ContentPasted0" style="margin:0px">And a general newbie question. You choose a distance of 3 as the default cutoff. In the computational protein-protein modeling world, is this
considered good evidence of contact between two proteins. The reason I ask is that I have discovered wild type and mutant alleles of a MYB protein which were modeled with Alphafold multimer along with its functional beta helix-loop-helix protein partner.
If I see changes in distances might that suggest changes in interaction capacity of any sort?</span></div>
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<span class="x_elementToProof" style="font-size:12pt; margin:0px"><span class="x_ContentPasted0" style="margin:0px">Phil McClean</span></span><br class="">
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<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_Apple-converted-space"> </span>Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Tuesday, October 4, 2022 11:57 AM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>McClean, Phillip <<a href="mailto:phillip.mcclean@ndsu.edu" class="">phillip.mcclean@ndsu.edu</a>><br class="">
<b class="">Cc:</b><span class="x_Apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a> <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [chimerax-users] alphafold contacts output file</font>
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<font size="3" class="">Hi Phil,</font>
<div class=""><font size="3" class=""><br class="">
</font></div>
<div class=""><font size="3" class=""> If you start ChimeraX by clicking an icon then it puts files on your desktop. If you start it from a shell (for example on Linux) it will put the files in the directory you started in. To find the directory ChimeraX
is currently in use the ChimeraX pwd command</font></div>
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</font></div>
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<div class="x_x_cxcmd" style="font-weight:bold; margin-top:0.5em; background-color:rgb(221,221,221); font-family:"Times New Roman"; font-variant-ligatures:normal; orphans:2; widows:2">
<div class="x_x_cxcmd_as_cmd" style="display:inline"><a href="" class=""><font size="3" class="">pwd</font></a></div>
</div>
<span class="" style="font-family:"Times New Roman"; font-variant-ligatures:normal; orphans:2; widows:2"><font size="3" class="">Current working directory is: /Users/goddard/Desktop</font></span></div>
<div class="">
<div class="" style="orphans:2; widows:2"><font size="3" class=""><br class="">
</font></div>
<div class=""><font size="3" class="">To change the directory ChimeraX is currently in use the cd command</font></div>
<div class=""><font size="3" class=""><br class="">
</font></div>
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<div class="x_x_cxcmd" style="font-weight:bold; margin-top:0.5em; background-color:rgb(221,221,221); font-family:"Times New Roman"; font-variant-ligatures:normal; orphans:2; widows:2">
<div class="x_x_cxcmd_as_cmd" style="display:inline"><a href="" class=""><font size="3" class="">cd ~/Documents</font></a></div>
</div>
<span class="" style="font-family:"Times New Roman"; font-variant-ligatures:normal; orphans:2; widows:2"><font size="3" class="">Current working directory is: /Users/goddard/Documents</font></span></div>
<div class="">
<div class="" style="orphans:2; widows:2"><font size="3" class=""><br class="">
</font></div>
<div class="" style="orphans:2; widows:2"><font size="3" class="">Lastly you can give a full path to the output file in your command</font></div>
<div class="" style="orphans:2; widows:2"><font size="3" class=""><br class="">
</font></div>
<div class="" style="orphans:2; widows:2"><font size="3" class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>alphafold contacts /B to /C output /Users/goddard/contact_pae.txt</font></div>
<div class="" style="orphans:2; widows:2"><font size="3" class=""><br class="">
</font></div>
<div class="" style="orphans:2; widows:2"><font size="3" class="">or</font></div>
<div class="" style="orphans:2; widows:2"><font size="3" class=""><br class="">
</font></div>
<div class="" style="orphans:2; widows:2">
<div class=""><font size="3" class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>alphafold contacts /B to /C output ~/contact_pae.txt</font></div>
<div class=""><font size="3" class=""><br class="">
</font></div>
</div>
<div class="" style="orphans:2; widows:2"><font size="3" class="">where "~" means your user account home directory.</font></div>
<div class="" style="orphans:2; widows:2"><font size="3" class=""><br class="">
</font></div>
<div class="" style="orphans:2; widows:2"><font size="3" class=""><font face="Times New Roman" class=""> <span class="x_Apple-converted-space"> </span></font> Tom</font></div>
<div class="" style="orphans:2; widows:2"><font face="Times New Roman" size="3" class=""><br class="">
</font></div>
<blockquote type="cite" class="">
<div class="">On Oct 4, 2022, at 9:21 AM, McClean, Phillip via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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Hi Everyone-</div>
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I used the following command to obtain a file with the contacts between two chains:</div>
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<pre class="x_x_ContentPasted0">alphafold contacts /B to /C output contact_pae.txt</pre>
I cannot seem to find where the output file is located.</div>
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Thanks for any help.</div>
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Phil McClean</div>
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">ChimeraX-users
mailing list</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px">ChimeraX-users@cgl.ucsf.edu</a><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
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subscription:</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div>
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