I have tried clicking the &#39;Open in Coot&#39; and &#39;Open in Pymol&#39; buttons <br>I saw a small window saying &quot;The .pdb file &quot;$s&quot; does not exist.&quot; I have not been able to get that small window to appear again.<br>
However, when clicking Open in Pymol...<br>The Pymol window spits this.<br>ExecutiveProcessPDBFile-Error: Unable to open file &#39;/Volumes/RAID1/...../coot-povray.pdb&#39;.<br><br>Phenix shows this in the window.<br>A Python error was detected.  This is probably a bug; click &quot;OK&quot; to send a bug report to the PHENIX developers.<br>
<br><br><br>Exception : XMLRPC error: &lt;Fault 1: &#39;pymol.CmdException:&lt;pymol.CmdException instance at 0x11690d878&gt;&#39;&gt;<br>Method: load_refinement<br>Params: /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_1/coot-povray, False<br>
<br><br>Traceback (most recent call last):<br>  File &quot;/usr/local/phenix-1.6.1-357/phenix/wxGUI2/App.py&quot;, line 569, in OnTimer<br>    self.pymol_server.flush_requests()<br>  File &quot;/usr/local/phenix-1.6.1-357/cctbx_project/libtbx/xmlrpc_utils.py&quot;, line 208, in flush_requests<br>
    return self._server.flush_requests()<br>  File &quot;/usr/local/phenix-1.6.1-357/cctbx_project/libtbx/xmlrpc_utils.py&quot;, line 126, in flush_requests<br>    (str(e), str(methodname), &quot;, &quot;.join([ str(p) for p in params ])))<br>
Exception: XMLRPC error: &lt;Fault 1: &#39;pymol.CmdException:&lt;pymol.CmdException instance at 0x11690d878&gt;&#39;&gt;<br>Method: load_refinement<br>Params: /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_1/coot-povray, False<br>
<br><br><br><br><br><div class="gmail_quote">On Mon, Jun 14, 2010 at 4:32 PM, Nathaniel Echols <span dir="ltr">&lt;<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">On Mon, Jun 14, 2010 at 12:20 PM, Ben Eisenbraun <span dir="ltr">&lt;<a href="mailto:bene@hkl.hms.harvard.edu" target="_blank">bene@hkl.hms.harvard.edu</a>&gt;</span> wrote:<br></div><div class="gmail_quote">
<div class="im"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
So first off I see that I somehow got an older version of Coot lodged in my<br>
~/.phenix/prefs.params file.  It was pointing to a linux Coot 0.6.1 32-bit<br>
installation.  I assume that will override the phenix.find_coot_command?<br></blockquote><div><br></div></div><div>Yes, there has to be some way to override automatic behavior.  (For instance, I&#39;m using this right now to prevent Phenix from using the Coot installed by Fink, because Fink has broken on my computer, yet again.)</div>
<div class="im">
<div><br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">The Mac problems appear to have cleared up when I removed the hard-coded<br>

path to the linux version of Coot in my preferences file.<br></blockquote><div><br></div></div><div>Sorry, I hadn&#39;t thought about cross-platform issues when I set this up; not sure if there&#39;s a good way to deal with this.  I don&#39;t think there are too many people running Linux+Mac environments with shared home directories, but I&#39;ve been worried about 32- vs. 64-bit compatibility.</div>

<div><br></div><div>-Nat</div></div>
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