<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Sumitro,<div><span class="Apple-tab-span" style="white-space:pre"> </span>I was unable to reproduce your error. I used 98 models on my Mac (9506 pairs) without problem, and 39 models on an XP machine here in the lab and they both worked fine. I asked about your version because the error message ("CloneMenu failed inside of MenuAddOrInsert") is mildly suggestive that it's a problem rebuilding one of the dynamic menus (e.g. Chain menu or Residue menu) as models are opened and closed, and we fixed a problem with that a few versions back.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Nonetheless my best guess is that the problem is still something along those lines, so my suggestion would be to just open all 39 files and do the matching between pairs without constantly opening and closing structures. I have attached a Python script that will go through all pairs of open models and run the "match" commands you were using. Perhaps you can use the script as is or modify it to suit your purposes. You run it (once you've opened your models) simply by opening it with File...Open or with the "open" command.</div><div><br></div><div>--Eric<br><div><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><div></div></div></div></div></body></html>