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Re: [ccp4bb] CCP4 6.1.0 Balbes error |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: CCP4 6.1.0 Balbes error From: "Dr {- dot -} F Long" fei {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2009-06-11 Dear Victor and Ronan, BALBES has a new version (1.0.0), with substantial changes in organization and functionality, implemented on the YORK web server very recently, you will expect to hear the announcement for that from Garib very soon. In the new version, the module 'subprocess' or 'popen2' will be imported depending on the version of python you are using (in PYTHON, early version of 2.3.0 or below without module "subprocess", version 2.4-2.6 "subprocees" and "popen2" both exist, and version 3.0 above "popen2" deprecated). The release of BALBES version 1.0.0 under CCP4 will be a little later Kind regards, Fei ___________________________________________________ Dr. Fei Long Tel: +44 1904 328252 Structural Biology Lab. Fax: +44 1904 328266 Department of Chemistry email: fei@ysbl.york.ac.uk University of York YORK, YO10 5YW, UK ___________________________________________________ 2009/6/11 Ronan Keegan > Dear Victor, > > Are you using python 3 by any chance? Balbes makes use of the popen2 > function for running the underlying CCP4 programs but this is replaced by > the subprocess function in python 3. We'll be updating Balbes to reflect > this change but in the mean time you should try installing an older python > such as python 2.6. > > Kind regards, > > Ronan > > Ronan Keegan > CCP4 Group > > > Victor Alves wrote: >> >> Dear BB >> >> Balbes (run from within CCP4i) gave me one MR solution but stopped with >> this error. >> >> I am now using the Balbes WWW server, but could some of you >> knowledgeable guys have some ideas of might be going on? >> >> Thanks >> >> Victor Alves >> >> Some info from log file: >> >> BALBES Version is 0.0.1.Mar_31_2008 JOB STARTS AT Mon Jun 8 18:02:06 >> 2009 >> >> ................ >> >> * Information from CCP4Interface script >> >> *************************************************************************** >> The program run with >> command: >> /usr/local/xtal/ccp4/ccp4-6.1.1/share/balbes/BALBES_0.0.1/bin_py/balbes >> OUT_ROOTDIR /home/victor/xtalwork/OlpA-M10/2_balbes NAME_ROOT 2_balbes >> HKLIN /home/victor/xtalwork/OlpA-M10/olpa_m10_scala_I4122.mtz SEQIN >> /home/victor/xtalwork/OlpA-M10/olpa_m10_info/OlpA_M10.seq XYZOUT >> /home/victor/xtalwork/OlpA-M10/olpa_m10_balbes_out1.pdb HKLOUT >> /home/victor/xtalwork/OlpA-M10/olpa_m10_balbes_out1.mtz has failed with >> error message >> >> /usr/local/xtal/ccp4/ccp4-6.1.1/share/balbes/BALBES_0.0.1/bin_py/balbes:22: >> DeprecationWarning: The popen2 module is deprecated. Use the subprocess >> module. >> import popen2, select, fcntl >> >> *************************************************************************** >> >> >> #CCP4I TERMINATION STATUS 0 >> >> "/usr/local/xtal/ccp4/ccp4-6.1.1/share/balbes/BALBES_0.0.1/bin_py/balbes:22: >> DeprecationWarning: The popen2 module is deprecated. Use the subprocess >> module. import popen2, select, fcntl" >> #CCP4I TERMINATION TIME 08 Jun 2009 18:23:47 >> #CCP4I MESSAGE Task failed >> >> > CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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