3v Running Log for JobId '2017.dec06.7c4'

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  • host ip address=128.114.150.252 (Wed Dec 6 17:49:10 2017)
  • converting pdb into xyzr (Wed Dec 6 17:49:10 2017)
  • completed conversion of PDB file: 2017.dec06.7c4.pdb (size: 5527k) (Wed Dec 6 17:50:38 2017)
  • converted 176860 atoms of 176860 atoms (Wed Dec 6 17:50:38 2017)
  • found 176860 atoms in pdb (Wed Dec 6 17:50:38 2017)
  • running 3v solvent program (Wed Dec 6 17:50:38 2017)
  • imaging volume (download mrc) with UCSF Chimera (Wed Dec 6 17:51:17 2017)
  • UCSF Chimera created Jmol compatible file (Wed Dec 6 17:52:37 2017)
  • compressing 2017.dec06.7c4.obj (Wed Dec 6 17:52:37 2017)
  • UCSF Chimera completed in 1 min 30 sec (Wed Dec 6 17:52:46 2017)
  • analyzing volume (Wed Dec 6 17:52:46 2017)
  • normal CoM (-82.3, 25.6, 13.0) Å (Wed Dec 6 17:53:14 2017)
  • reduced center failed (Wed Dec 6 17:53:18 2017)
  • volume analysis completed in 32.21 sec (Wed Dec 6 17:53:18 2017)
  • compressing 2017.dec06.7c4.mrc (Wed Dec 6 17:53:18 2017)
  • FINISHED (Wed Dec 6 17:53:19 2017)

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Log file display

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Terminal display
		
Message: converting pdb into xyzr 
/var/www/html/output/2017/dec06/7c4 
Message: completed conversion of PDB file: 2017.dec06.7c4.pdb (size: 5527k) 
Message: converted 176860 atoms of 176860 atoms 
Message: found 176860 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2017/dec06/7c4/2017.dec06.7c4.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2017.dec06.7c4.obj 
Message: UCSF Chimera completed in 1 min 30 sec 
OBJFILE /var/www/html/3vee/output/2017/dec06/7c4/2017.dec06.7c4.obj.gz 
Message: analyzing volume 
Message: normal CoM (-82.3, 25.6, 13.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 32.21 sec 
Message: compressing 2017.dec06.7c4.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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