<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi André,<div class=""><br class=""></div><div class=""><span style="font-family: Verdana, Arial, "Bitstream Vera Sans", Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);" class="">I added two options "replace" (default true) and "name" (default "PAE Contacts") to the alphafold contacts command. The replace option determines if existing contact pseudobonds (in the group with the specified or default name) are deleted. If replace is false the new contacts are just added to any existing ones. The name option gives the pseudobond model the specified name. So you could use </span></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class=""><br class=""></span></font></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class="">alphafold contacts /A to /B</span></font></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class="">alphafold contacts /B to /C replace false</span></font></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class="">alphafold contacts /A to /C replace false</span></font></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class=""><br class=""></span></font></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class="">to put all the contacts in one pseudobond submodel. If instead you wanted them in 3 different models you could use</span></font></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class=""><br class=""></span></font></div><div class=""><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class="">alphafold contacts /A to /B name "AB contacts"</span></font></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class="">alphafold contacts /B to /C name "BC contacts"</span></font></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class="">alphafold contacts /A to /C name "AC contacts"</span></font></div></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class=""><br class=""></span></font></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class="">This will be in tomorrow's (Oct 11) ChimeraX daily builds.</span></font></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class=""><br class=""></span></font></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</span></font></div><div class=""><font face="Verdana, Arial, Bitstream Vera Sans, Helvetica, sans-serif" size="2" class=""><span style="background-color: rgb(255, 255, 255);" class=""><br class=""></span></font></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 10, 2022, at 12:38 PM, Michaelis, Andre Clemens <<a href="mailto:michaelis@biochem.mpg.de" class="">michaelis@biochem.mpg.de</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" class="">
<div dir="auto" class="">
Awesome,
<div class="">Thank you so much!<br class="">
<br class="">
<div dir="ltr" class=""><div style="margin: 0cm 0cm 0.0001pt;" class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">Best </span></div><div style="margin: 0cm 0cm 0.0001pt;" class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">André<o:p class=""></o:p></span></div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt;"><span style="background-color: rgba(255, 255, 255, 0);" class=""> </span><span style="font-size: 13pt; background-color: rgba(255, 255, 255, 0);" class=""> </span></p><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt;"><span style="background-color: rgba(255, 255, 255, 0);" class=""><span lang="EN-US" class=""> </span></span></p><div style="margin: 0cm 0cm 0.0001pt;" class=""><span style="background-color: rgba(255, 255, 255, 0);" class=""><span lang="EN-US" class="">——————————————————</span><span lang="EN-US" class=""><br class="">
<br class="">
</span></span></div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt;"></p>
</div>
<div dir="ltr" class=""><br class="">
<blockquote type="cite" class="">Am 10.10.2022 um 20:50 schrieb Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>>:<br class="">
<br class="">
</blockquote>
</div>
<blockquote type="cite" class="">
<div dir="ltr" class=""> Hi André,
<div class=""><br class="">
</div>
<div class=""> The "alphafold contacts" command creates a submodel of the atomic structure containing pseudobonds with the submodel named "PAE Contacts". If you rename that submodel then it won't replace it when you do the second alphafold contacts command
on the same structure. For instance, if the structure is model #1.</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>alphafold contacts /A to /B</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>rename #1.1 "AB contacts"</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>alphafold contacts /B to /C</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>rename #1.2 "BC contacts"</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>alphafold contacts /A to /C</div>
<div class=""><br class="">
</div>
<div class="">This should be easier to do. I should add an option to the alphafold contacts command "replace false" that automatically uses new names for each group of pseudobonds. I've made a request for this.</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span><a href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7770" class="">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7770</a></div>
<div class=""><br class="">
</div>
<div class=""> Tom<br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Oct 10, 2022, at 5:47 AM, Michaelis, Andre Clemens via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;">
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">Hi,<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">Is it possible to draw contacts (PAE, alphafold) between more than just 2 subunits?<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">e.g.:<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">alphafold contacts /A to /B<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">AND<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">alphafold contacts /B to /C<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">AND<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">alphafold contacts /A to /C<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">Righ now, a new command deletes the old contacts. Not sure about a syntax that would combine/add those<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">Thank you very much!<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class="">Best André<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" class=""><o:p class=""> </o:p></span></div>
</div>
<span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">ChimeraX-users
mailing list</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu" 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; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ChimeraX-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Manage
subscription:</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" 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; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div>
</blockquote>
</div>
<br class="">
</div>
</div>
</blockquote>
</div>
</div>
</div></blockquote></div><br class=""></div></body></html>