<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 Ibrahim,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>I'm not sure what part of my previous answer was unclear. Writing such a script would be very, very hard because the trajectory reading/analysis code was not designed for scripting. So effectively the answer is no, there is no way to cluster from a DCD using a script with Chimera.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 16, 2020, at 10:35 AM, Ibrahim Mohamed <<a href="mailto:hollow_ichigo199799@yahoo.com" class="">hollow_ichigo199799@yahoo.com</a>> wrote:</div><br class="Apple-interchange-newline"><div style="direction: rtl;" class=""><div class=""><div class="ydpde0ab3c2yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:16px;"><div class=""></div>
<div dir="ltr" data-setdir="false" class="">can you provide me, if it is possible, with the script of clustering from dcd file?<br class=""> i am thinking about running the script only on google colab after i upload the files (dcd and psf). Since colab has a larger RAM Maybe it will work.</div><div class=""><br class=""></div>
</div><div id="yahoo_quoted_5528237377" class="yahoo_quoted">
<div style="font-family:'Helvetica Neue', Helvetica, Arial, sans-serif;font-size:13px;color:#26282a;" class="">
<div class="">
بتاريخ الخميس، 16 تموز 2020 07:04:21 م غرينتش+2، Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> كتب:
</div>
<div class=""><br class=""></div>
<div class=""><br class=""></div>
<div class=""><div id="yiv6132126485" class=""><div class="">Hi Ibrahim,<div class="yiv6132126485"><span class="yiv6132126485Apple-tab-span" style="white-space:pre;"> </span>Sorry, but this is way too hard. That part of Chimera simply was not designed for scripting. ChimeraX is much better at allowing scripting, but it doesn't have the clustering functionality you need.</div><div class="yiv6132126485"><span class="yiv6132126485Apple-tab-span" style="white-space:pre;"> </span></div><div class="yiv6132126485"><div class="yiv6132126485">--Eric</div><div class="yiv6132126485"><br clear="none" class="yiv6132126485"></div><div class="yiv6132126485"><span class="yiv6132126485Apple-tab-span" style="white-space:pre;"> </span>Eric Pettersen</div><div class="yiv6132126485"><span class="yiv6132126485Apple-tab-span" style="white-space:pre;"> </span>UCSF Computer Graphics Lab</div><div class="yiv6132126485"><br clear="none" class="yiv6132126485"></div><div class=""><br clear="none" class="yiv6132126485"><blockquote class="yiv6132126485" type="cite"><div class="yiv6132126485yqt8988685582" id="yiv6132126485yqt74976"><div class="yiv6132126485">On Jul 16, 2020, at 5:05 AM, Ibrahim Mohamed <<a rel="nofollow" shape="rect" class="yiv6132126485" ymailto="mailto:hollow_ichigo199799@yahoo.com" target="_blank" href="mailto:hollow_ichigo199799@yahoo.com">hollow_ichigo199799@yahoo.com</a>> wrote:</div><br clear="none" class="yiv6132126485Apple-interchange-newline"><div class="yiv6132126485"><div class="yiv6132126485"><div class="yiv6132126485yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:16px;"><div class="yiv6132126485" dir="ltr">Greeting sir, <br clear="none" class="yiv6132126485">i want to use chimera (V 1.14) on a super computer to cluster the results from NAMD .dcd file but i found that it can be used only through the GUI.<br clear="none" class="yiv6132126485">Is there a way to cluster the results from .dcd file using a script? <br clear="none" class="yiv6132126485">if it is possible please send me the script<br clear="none" class="yiv6132126485">thanks</div></div></div>_______________________________________________<br clear="none" class="yiv6132126485">Chimera-users mailing list: <a rel="nofollow" shape="rect" class="yiv6132126485" ymailto="mailto:Chimera-users@cgl.ucsf.edu" target="_blank" href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br clear="none" class="yiv6132126485">Manage subscription: <a rel="nofollow" shape="rect" class="yiv6132126485" target="_blank" href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br clear="none" class="yiv6132126485"></div></div></blockquote></div><br clear="none" class="yiv6132126485"></div></div></div></div>
</div>
</div></div>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>