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<span class="elementToProof ContentPasted0" style="font-size:12pt;margin:0px">Hi Tom,</span>
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<div class="elementToProof ContentPasted0" style="font-size:12pt;margin:0px">Thanks. Found it on the desktop.</div>
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<div class="elementToProof" style="font-size:12pt;margin:0px"><span style="margin:0px" class="ContentPasted0">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="ContentPasted0">
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</span></div>
<div class="elementToProof" style="font-size:12pt;margin:0px"><span style="margin:0px" class="ContentPasted0">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="elementToProof" style="font-size:12pt;margin:0px"><span style="margin:0px" class="ContentPasted0">Phil McClean</span></span><br>
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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 11:57 AM<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"><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_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_cxcmd_as_cmd" style="display:inline"><a href="" class=""><font size="3" class="">pwd</font></a></div>
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<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>
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</font></div>
<div><font size="3" class="">To change the directory ChimeraX is currently in use the cd command</font></div>
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</font></div>
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<div class="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_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>
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</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>
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</font></div>
<div class="" style="orphans:2; widows:2"><font size="3" class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>alphafold contacts /B to /C output /Users/goddard/contact_pae.txt</font></div>
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</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_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>
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<div class="" style="orphans:2; widows:2"><font size="3" class="">where "~" means your user account home directory.</font></div>
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<div class="" style="orphans:2; widows:2"><font size="3" class=""><font face="Times New Roman" class="">
</font> Tom</font></div>
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<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_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; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; 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">
<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">Manage
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; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div>
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