<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Raag,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>All Matej’s suggestions are excellent. In addition, there are two more things I can think of. One, you might consider using Chimera’s “Report A Bug” entry in the Help menu to send us a bug report (and attach the .gro file) — there may be something I can do about it. The other thing is to make sure your are using the 64-bit version of Chimera — it can handle larger systems than the 32-bit version.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div apple-content-edited="true" class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><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>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Oct 9, 2015, at 12:29 AM, Repic Matej <<a href="mailto:matej.repic@epfl.ch" class="">matej.repic@epfl.ch</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">Hi Raag,<br class=""><br class="">Chimera is not really efficient with big files (many atoms), but you can<br class="">try a few of these:<br class=""><br class="">1) run on a machine with lots of ram<br class="">2) avoid as many atoms as possible<br class="">3) match as few atoms as possible<br class="">4) avoid rendering the file<br class="">5) if you want to have it rendered, disable smart display (Chimera pref ><br class="">New Molecules > Smart Initial Display)<br class=""><br class="">Ad 4) Write a command line chimera script (run with "chimera --nogui<br class="">script.cmd"), for example:<br class="">-----script.cmd------<br class="">open file1.gro file2.pdb<br class="">match #0:res #1:res<br class="">write format pdb relative 1 0 aligned.pdb<br class="">---------------------<br class=""><br class="">Best,<br class=""><br class=""><br class=""><br class=""><br class="">------------------------------------------------------<br class="">Dr. Matej Repic<br class="">Ecole Polytechnique Fédérale de Lausanne<br class="">Laboratory of Computational Chemistry and Biochemistry<br class="">SB - ISIC LCBC<br class="">BCH 4108<br class="">CH - 1015 Lausanne<br class="">------------------------------------------------------<br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class="">On 10/9/15, 08:54, "<a href="mailto:chimera-users-bounces@cgl.ucsf.edu" class="">chimera-users-bounces@cgl.ucsf.edu</a> on behalf of Raag<br class="">Saluja" <<a href="mailto:chimera-users-bounces@cgl.ucsf.edu" class="">chimera-users-bounces@cgl.ucsf.edu</a> on behalf of<br class=""><a href="mailto:saluja.raag@gmail.com" class="">saluja.raag@gmail.com</a>> wrote:<br class=""><br class=""><blockquote type="cite" class="">Hi!<br class=""><br class="">Chimera crashes when I try to open a .gro file (created through GROMACS).<br class=""><br class="">I wanted to open the .gro file and then superimpose it on a .pdb file.<br class=""><br class="">Can you please guide? Thank you!<br class=""><br class="">Regards,<br class="">Raag<br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list<br class=""><a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list<br class=""><a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br class=""><br class=""></div></blockquote></div><br class=""></div></body></html>