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

RaDaniel Christian 성준 rendereason at gmail.com
Fri Jun 18 15:47:16 PDT 2010


I have setup the Full Path to Coot in preferences setup as
/sw64/bin/coot

On Fri, Jun 18, 2010 at 5:45 PM, RaDaniel Christian 성준 <
rendereason at gmail.com> wrote:

> 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 <
> rendereason at 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 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
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
>>
>>
>> --
>> 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)
>>
>
>
>
> --
> 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)
>



-- 
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)
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