[ccp4bb] PHENIX question

- Protein crystallography

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- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

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   - Amino Acids

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: about microbatch
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2008-07-26

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Subject: Re: PHENIX question
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-07-26

Subject: PHENIX question
From: aberndt {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK aberndt {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2008-07-26

Dear Phenix Programmers/Users,

after running a 'fink selfupdate' on OS X 10.5.2 (Xquartz 2.2.3) I am no
longer able to use my Phenix Suite (Ver 1.3 of 26-05-2008) . It crashes
everytime with obscure (at least to me) error messages (see below).

Does anyone have a clue as to how to proceed and maybe fix it?

Thanks very much in advance!

Alex Berndt
MRC-LMB
aberndt@mrc-lmb.cam.ac.uk

Python(78825,0xb0185000) malloc: *** mmap(size=4083712) failed (error
code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
set meta data failed
Traceback (most recent call last):
File "/usr/local/phenix-1.3-rc2/phenix/wxGUI/wxtask.py", line 522, in
OnGoButton
try: self.parent.OnGo()
File "/usr/local/phenix-1.3-rc2/phenix/wxGUI/Dialogs.py", line 470, in OnGo
gp.RunStrategy()
File "/usr/local/phenix-1.3-rc2/phenix/wxGUI/BMPTaskCanvas.py", line
1170, in RunStrategy
self.RunRemotely()
File "/usr/local/phenix-1.3-rc2/phenix/wxGUI/BMPTaskCanvas.py", line
1293, in RunRemotely
prefs = PDSServerClient.GetPreferences()
File "/usr/local/phenix-1.3-rc2/phenix/phenix/server/PhenixClient.py",
line 201, in GetPreferences
return self._remote_call('GetPreferences',arg,kw)
File "/usr/local/phenix-1.3-rc2/phenix/phenix/server/PhenixClient.py",
line 449, in _remote_call
cPickle.dump(all,self.send,1)
File
"/usr/local/phenix-1.3-rc2/build/mac-intel-osx/base/Python.framework/Versions/2.5/lib/python2.5/socket.py",
line 262, in write
self.flush()
File
"/usr/local/phenix-1.3-rc2/build/mac-intel-osx/base/Python.framework/Versions/2.5/lib/python2.5/socket.py",
line 249, in flush
self._sock.sendall(buffer)
socket.error: (32, 'Broken pipe'

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: about microbatch
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2008-07-26

Next message:
Subject: Re: PHENIX question
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-07-26