Re: [ccp4bb] CCP4 6.1.0 Balbes error
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
Re: [ccp4bb] CCP4 6.1.0 Balbes error
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: f...@ysbl.york.ac.uk University of York YORK, YO10 5YW, UK ___ 2009/6/11 Ronan Keegan ronan.kee...@stfc.ac.uk: 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
Re: [ccp4bb] CCP4 6.1.0 Balbes error
Thank you both Actually, I am using Ubuntu 9.04 Linux and 'python' at the terminal gives me version 2.6.2. In fact the system has both versions 2.5 and 2.6 (I think 2.5 comes from the previous Ubuntu 8.10, before I upgraded). Ok. I'll wait for the new BALBES version because on the downloads page there is still a May 24 version (BALBES_0.0.1). Meanwhile I already got the results from the www server (nice results, I might add :-) Bye Victor Alves __ VICTOR DIOGO ALVES, DVM PhD Professor Auxiliar Faculdade de Medicina Veterinária UTL - Lisboa __ -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Dr. F Long Sent: quinta-feira, 11 de Junho de 2009 12:39 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 6.1.0 Balbes error 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: f...@ysbl.york.ac.uk University of York YORK, YO10 5YW, UK ___ 2009/6/11 Ronan Keegan ronan.kee...@stfc.ac.uk: 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
