[phenixbb] "Open in Coot" not working on 1.6.1-357

RaDaniel Christian 성준 rendereason at gmail.com
Fri Jun 18 14:49:52 PDT 2010

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

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
  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 at lbl.gov> wrote:

> On Mon, Jun 14, 2010 at 12:20 PM, Ben Eisenbraun <bene at 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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