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

Open In Coot opens the splash window, but nothing else happens. 'which coot' returns /sw64/bin/coot I was mistaken about Pymol. Open In Pymol works. I just had to re-run the refinement, and Pymol opened the file ok. Daniel On Fri, Jun 18, 2010 at 4:49 PM, RaDaniel Christian 성준 < [email protected]> 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: '> 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: '> 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 wrote:

...

On Mon, Jun 14, 2010 at 12:20 PM, Ben Eisenbraun < [email protected]> 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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Choel Kim Structural Biology Laboratory Department of Pharmacology, Baylor College of Medicine, Alkek N510, One Baylor Plaza, Houston, TX 77030 713-798-8687 (Lab) 713-798-3145 (Fax)

-- Stop the ACTA. Row, row; fight the power! http://www.eff.org/ Choel Kim Structural Biology Laboratory Department of Pharmacology, Baylor College of Medicine, Alkek N510, One Baylor Plaza, Houston, TX 77030 713-798-8687 (Lab) 713-798-3145 (Fax)