3v Running Log for JobId '2019.jun09.bbb'

Program is still running, progress is shown below

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  • host ip address=124.17.103.130 (Mon Jun 10 01:18:23 2019)
  • converting pdb into xyzr (Mon Jun 10 01:18:23 2019)
  • completed conversion of PDB file: 2019.jun09.bbb.pdb (size: 197k) (Mon Jun 10 01:18:26 2019)
  • converted 6310 atoms of 6310 atoms (Mon Jun 10 01:18:26 2019)
  • found 6310 atoms in pdb (Mon Jun 10 01:18:26 2019)
  • running 3v volume program (Mon Jun 10 01:18:26 2019)
  • smoothing out volume (Mon Jun 10 01:18:26 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Jun 10 01:18:26 2019)
  • UCSF Chimera created Jmol compatible file (Mon Jun 10 01:18:36 2019)
  • compressing 2019.jun09.bbb.obj (Mon Jun 10 01:18:36 2019)
  • UCSF Chimera completed in 9.95 sec (Mon Jun 10 01:18:36 2019)
  • analyzing volume (Mon Jun 10 01:18:36 2019)
  • normal CoM (-0.5, 0.3, -6.6) Å (Mon Jun 10 01:18:38 2019)
  • reduced center failed (Mon Jun 10 01:18:38 2019)
  • volume analysis completed in 2.47 sec (Mon Jun 10 01:18:38 2019)
  • compressing 2019.jun09.bbb.mrc (Mon Jun 10 01:18:38 2019)
  • FINISHED (Mon Jun 10 01:18:38 2019)

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Log file display

Show last lines of log file 
Terminal display
		
/srv/output/2019/jun09/bbb 
Message: completed conversion of PDB file: 2019.jun09.bbb.pdb (size: 197k) 
Message: converted 6310 atoms of 6310 atoms 
Message: found 6310 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/jun09/bbb/2019.jun09.bbb.mrc 
Message: smoothing out volume 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2019.jun09.bbb.obj 
Message: UCSF Chimera completed in 9.95 sec 
OBJFILE /var/www/html/3vee/output/2019/jun09/bbb/2019.jun09.bbb.obj.gz 
Message: analyzing volume 
Message: normal CoM (-0.5, 0.3, -6.6) Å 
Message: reduced center failed 
Message: volume analysis completed in 2.47 sec 
Message: compressing 2019.jun09.bbb.mrc 
Message: FINISHED 
		


Citation:
'3V: cavity, channel and cleft volume calculator and extractor' (free text)
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W555–W562
by Neil R. Voss and Mark Gerstein
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If you find this useful or want more functionality please contact Neil <vossman77 [at] gmail [dot] com>
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