3v Running Log for JobId '2018.jan07.7f0'

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  • host ip address=37.170.63.99 (Sun Jan 7 10:14:01 2018)
  • converting pdb into xyzr (Sun Jan 7 10:14:01 2018)
  • completed conversion of PDB file: 2018.jan07.7f0.pdb (size: 119k) (Sun Jan 7 10:14:02 2018)
  • converted 3793 atoms of 3793 atoms (Sun Jan 7 10:14:02 2018)
  • found 3793 atoms in pdb (Sun Jan 7 10:14:02 2018)
  • running 3v volume program (Sun Jan 7 10:14:02 2018)
  • smoothing out volume (Sun Jan 7 10:14:03 2018)
  • imaging volume (download mrc) with UCSF Chimera (Sun Jan 7 10:14:03 2018)
  • UCSF Chimera created Jmol compatible file (Sun Jan 7 10:14:11 2018)
  • compressing 2018.jan07.7f0.obj (Sun Jan 7 10:14:11 2018)
  • UCSF Chimera completed in 8.79 sec (Sun Jan 7 10:14:11 2018)
  • analyzing volume (Sun Jan 7 10:14:11 2018)
  • normal CoM (-9.6, -4.6, 9.0) Å (Sun Jan 7 10:14:13 2018)
  • reduced center failed (Sun Jan 7 10:14:13 2018)
  • volume analysis completed in 1.45 sec (Sun Jan 7 10:14:13 2018)
  • compressing 2018.jan07.7f0.mrc (Sun Jan 7 10:14:13 2018)
  • FINISHED (Sun Jan 7 10:14:13 2018)

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Log file display

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Terminal display
		
/var/www/html/output/2018/jan07/7f0 
Message: completed conversion of PDB file: 2018.jan07.7f0.pdb (size: 119k) 
Message: converted 3793 atoms of 3793 atoms 
Message: found 3793 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2018/jan07/7f0/2018.jan07.7f0.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 2018.jan07.7f0.obj 
Message: UCSF Chimera completed in 8.79 sec 
OBJFILE /var/www/html/3vee/output/2018/jan07/7f0/2018.jan07.7f0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-9.6, -4.6, 9.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.45 sec 
Message: compressing 2018.jan07.7f0.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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