On Fri, Jun 18, 2010 at 4:49 PM, RaDaniel Christian 성준 <rendereason@gmail.com> wrote:

I have tried clicking the 'Open in Coot' and 'Open in Pymol' buttons
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.
However, when clicking Open in Pymol...
The Pymol window spits this.
ExecutiveProcessPDBFile-Error: Unable to open file '/Volumes/RAID1/...../coot-povray.pdb'.

Phenix shows this in the window.
A Python error was detected. This is probably a bug; click "OK" to send a bug report to the PHENIX developers.

Exception : XMLRPC error: <Fault 1: 'pymol.CmdException:<pymol.CmdException instance at 0x11690d878>'>
Method: load_refinement
Params: /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_1/coot-povray, False

Traceback (most recent call last):
File "/usr/local/phenix-1.6.1-357/phenix/wxGUI2/App.py", line 569, in OnTimer
    self.pymol_server.flush_requests()
File "/usr/local/phenix-1.6.1-357/cctbx_project/libtbx/xmlrpc_utils.py", line 208, in flush_requests
    return self._server.flush_requests()
File "/usr/local/phenix-1.6.1-357/cctbx_project/libtbx/xmlrpc_utils.py", line 126, in flush_requests
    (str(e), str(methodname), ", ".join([ str(p) for p in params ])))
Exception: XMLRPC error: <Fault 1: 'pymol.CmdException:<pymol.CmdException instance at 0x11690d878>'>
Method: load_refinement
Params: /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_1/coot-povray, False

On Mon, Jun 14, 2010 at 4:32 PM, Nathaniel Echols <nechols@lbl.gov> wrote:

On Mon, Jun 14, 2010 at 12:20 PM, Ben Eisenbraun <bene@hkl.hms.harvard.edu> wrote:

So first off I see that I somehow got an older version of Coot lodged in my
~/.phenix/prefs.params file. It was pointing to a linux Coot 0.6.1 32-bit
installation. I assume that will override the phenix.find_coot_command?

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.)

The Mac problems appear to have cleared up when I removed the hard-coded
path to the linux version of Coot in my preferences file.

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.

-Nat

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