<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><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><div class=""><font size="3" class=""><br class=""></font></div><div class=""><div class="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; text-decoration-thickness: initial;"><div class="cxcmd_as_cmd" style="display: inline;"><a href="cxcmd:pwd" class=""><font size="3" class="">pwd</font></a></div></div><span style="font-family: "Times New Roman"; font-variant-ligatures: normal; orphans: 2; widows: 2; text-decoration-thickness: initial;" class=""><font size="3" class="">Current working directory is: /Users/goddard/Desktop</font></span></div><div class=""><div style="orphans: 2; widows: 2;" class=""><font size="3" class=""><br class=""></font></div><div><font size="3" class="">To change the directory ChimeraX is currently in use the cd command</font></div><div><font size="3" class=""><br class=""></font></div><div><div class="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; text-decoration-thickness: initial;"><div class="cxcmd_as_cmd" style="display: inline;"><a href="cxcmd:cd /Users/goddard/Documents" class=""><font size="3" class="">cd ~/Documents</font></a></div></div><span style="font-family: "Times New Roman"; font-variant-ligatures: normal; orphans: 2; widows: 2; text-decoration-thickness: initial;" class=""><font size="3" class="">Current working directory is: /Users/goddard/Documents</font></span></div><div><div style="orphans: 2; widows: 2;" class=""><font size="3" class=""><br class=""></font></div><div style="orphans: 2; widows: 2;" class=""><font size="3" class="">Lastly you can give a full path to the output file in your command</font></div><div style="orphans: 2; widows: 2;" class=""><font size="3" class=""><br class=""></font></div><div style="orphans: 2; widows: 2;" class=""><font size="3" class=""><span class="Apple-tab-span" style="white-space:pre"> </span>alphafold contacts /B to /C output /Users/goddard/contact_pae.txt</font></div><div style="orphans: 2; widows: 2;" class=""><font size="3" class=""><br class=""></font></div><div style="orphans: 2; widows: 2;" class=""><font size="3" class="">or</font></div><div style="orphans: 2; widows: 2;" class=""><font size="3" class=""><br class=""></font></div><div style="orphans: 2; widows: 2;" class=""><div class=""><font size="3" class=""><span class="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 style="orphans: 2; widows: 2;" class=""><font size="3" class="">where "~" means your user account home directory.</font></div><div style="orphans: 2; widows: 2;" class=""><font size="3" class=""><br class=""></font></div><div style="orphans: 2; widows: 2;" class=""><font size="3" class=""><font face="Times New Roman" class=""> </font> Tom</font></div><div style="orphans: 2; widows: 2;" class=""><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><br class="Apple-interchange-newline"><div class=""><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Hi Everyone-</div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">I used the following command to obtain a file with the contacts between two chains:</div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><pre class="ContentPasted0">alphafold contacts /B to /C output contact_pae.txt</pre>I cannot seem to find where the output file is located.</div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Thanks for any help.</div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br class=""></div><div class="elementToProof" style="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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Phil McClean</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></body></html>