I have setup the Full Path to Coot in preferences setup as<br>/sw64/bin/coot<br><br><div class="gmail_quote">On Fri, Jun 18, 2010 at 5:45 PM, RaDaniel Christian 성준 <span dir="ltr"><<a href="mailto:rendereason@gmail.com">rendereason@gmail.com</a>></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;">Open In Coot opens the splash window, but nothing else happens. 'which coot' returns<br>
/sw64/bin/coot<br><br>I was mistaken about Pymol. Open In Pymol works. I just had to re-run the refinement, and Pymol opened the file ok.<br>
<br>Daniel<div><div></div><div class="h5"><br><br><div class="gmail_quote">On Fri, Jun 18, 2010 at 4:49 PM, RaDaniel Christian 성준 <span dir="ltr"><<a href="mailto:rendereason@gmail.com" target="_blank">rendereason@gmail.com</a>></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;">
I have tried clicking the 'Open in Coot' and 'Open in Pymol' buttons <br>I saw a small window saying "The .pdb file "$s" does not exist." 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 '/Volumes/RAID1/...../coot-povray.pdb'.<br><br>Phenix shows this in the window.<br>A Python error was detected. This is probably a bug; click "OK" to send a bug report to the PHENIX developers.<br>
<br><br><br>Exception : XMLRPC error: <Fault 1: 'pymol.CmdException:<pymol.CmdException instance at 0x11690d878>'><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 "/usr/local/phenix-1.6.1-357/phenix/wxGUI2/App.py", line 569, in OnTimer<br> self.pymol_server.flush_requests()<br> File "/usr/local/phenix-1.6.1-357/cctbx_project/libtbx/xmlrpc_utils.py", line 208, in flush_requests<br>
return self._server.flush_requests()<br> File "/usr/local/phenix-1.6.1-357/cctbx_project/libtbx/xmlrpc_utils.py", line 126, in flush_requests<br> (str(e), str(methodname), ", ".join([ str(p) for p in params ])))<br>
Exception: XMLRPC error: <Fault 1: 'pymol.CmdException:<pymol.CmdException instance at 0x11690d878>'><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"><div><div></div><div>On Mon, Jun 14, 2010 at 4:32 PM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div>
<div>On Mon, Jun 14, 2010 at 12:20 PM, Ben Eisenbraun <span dir="ltr"><<a href="mailto:bene@hkl.hms.harvard.edu" target="_blank">bene@hkl.hms.harvard.edu</a>></span> wrote:<br></div><div class="gmail_quote">
<div><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'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>
<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't thought about cross-platform issues when I set this up; not sure if there's a good way to deal with this. I don't think there are too many people running Linux+Mac environments with shared home directories, but I've been worried about 32- vs. 64-bit compatibility.</div>
<div><br></div><div>-Nat</div></div>
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<br></div></blockquote></div><br><br clear="all"><div><br>-- <br>Stop the ACTA. Row, row; fight the power! <a href="http://www.eff.org/" target="_blank">http://www.eff.org/</a><br><br></div>Choel Kim Structural Biology Laboratory<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Stop the ACTA. Row, row; fight the power! <a href="http://www.eff.org/" target="_blank">http://www.eff.org/</a><br><br>Choel Kim Structural Biology Laboratory<br>Department of Pharmacology, Baylor College of Medicine,<br>
Alkek N510, One Baylor Plaza, Houston, TX 77030<br>713-798-8687 (Lab)<br>713-798-3145 (Fax)<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Stop the ACTA. Row, row; fight the power! <a href="http://www.eff.org/">http://www.eff.org/</a><br><br>Choel Kim Structural Biology Laboratory<br>Department of Pharmacology, Baylor College of Medicine,<br>
Alkek N510, One Baylor Plaza, Houston, TX 77030<br>713-798-8687 (Lab)<br>713-798-3145 (Fax)<br>