3v Running Log for JobId '2017.apr20.f71'

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  • host ip address=108.176.246.85 (Thu Apr 20 22:34:18 2017)
  • converting pdb into xyzr (Thu Apr 20 22:34:18 2017)
  • completed conversion of PDB file: 2017.apr20.f71.pdb (size: 148k) (Thu Apr 20 22:34:20 2017)
  • converted 4729 atoms of 4729 atoms (Thu Apr 20 22:34:20 2017)
  • found 4729 atoms in pdb (Thu Apr 20 22:34:20 2017)
  • running 3v volume program (Thu Apr 20 22:34:20 2017)
  • smoothing out volume (Thu Apr 20 22:34:28 2017)
  • imaging volume (download mrc) with UCSF Chimera (Thu Apr 20 22:34:28 2017)
  • UCSF Chimera created Jmol compatible file (Thu Apr 20 22:34:38 2017)
  • compressing 2017.apr20.f71.obj (Thu Apr 20 22:34:38 2017)
  • UCSF Chimera completed in 10.6 sec (Thu Apr 20 22:34:39 2017)
  • analyzing volume (Thu Apr 20 22:34:39 2017)
  • normal CoM (10.2, 0.6, -13.7) Å (Thu Apr 20 22:34:46 2017)
  • reduced center failed (Thu Apr 20 22:34:48 2017)
  • volume analysis completed in 9.16 sec (Thu Apr 20 22:34:48 2017)
  • compressing 2017.apr20.f71.mrc (Thu Apr 20 22:34:48 2017)
  • FINISHED (Thu Apr 20 22:34:48 2017)

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Log file display

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Terminal display
		
/var/www/html/output/2017/apr20/f71 
Message: completed conversion of PDB file: 2017.apr20.f71.pdb (size: 148k) 
Message: converted 4729 atoms of 4729 atoms 
Message: found 4729 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2017/apr20/f71/2017.apr20.f71.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 2017.apr20.f71.obj 
Message: UCSF Chimera completed in 10.6 sec 
OBJFILE /var/www/html/3vee/output/2017/apr20/f71/2017.apr20.f71.obj.gz 
Message: analyzing volume 
Message: normal CoM (10.2, 0.6, -13.7) Å 
Message: reduced center failed 
Message: volume analysis completed in 9.16 sec 
Message: compressing 2017.apr20.f71.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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