3v Running Log for JobId '2019.may15.e49'

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  • host ip address=130.160.200.4 (Wed May 15 13:53:20 2019)
  • downloading pdb file (Wed May 15 13:53:20 2019)
  • failed to download pdb id: 2nvh (Wed May 15 13:53:20 2019)
  • trying download pdb id again without bio unit (Wed May 15 13:53:23 2019)
  • completed download of PDB id 2nvh (size: 136 k, 1723 lines) (Wed May 15 13:53:23 2019)
  • converting pdb into xyzr (Wed May 15 13:53:23 2019)
  • completed conversion of PDB file: 2nvh-2019.may15.e49.pdb (size: 38k) (Wed May 15 13:53:24 2019)
  • converted 1224 atoms of 1224 atoms (Wed May 15 13:53:24 2019)
  • found 1224 atoms in pdb (Wed May 15 13:53:24 2019)
  • running 3v volume program (Wed May 15 13:53:24 2019)
  • smoothing out volume (Wed May 15 13:53:24 2019)
  • imaging volume (download mrc) with UCSF Chimera (Wed May 15 13:53:24 2019)
  • UCSF Chimera created Jmol compatible file (Wed May 15 13:53:31 2019)
  • compressing 2nvh-2019.may15.e49.obj (Wed May 15 13:53:31 2019)
  • UCSF Chimera completed in 7.08 sec (Wed May 15 13:53:31 2019)
  • analyzing volume (Wed May 15 13:53:31 2019)
  • normal CoM (1.0, -4.8, -7.4) Å (Wed May 15 13:53:32 2019)
  • reduced center failed (Wed May 15 13:53:32 2019)
  • volume analysis completed in 0.88 sec (Wed May 15 13:53:32 2019)
  • compressing 2nvh-2019.may15.e49.pdb (Wed May 15 13:53:32 2019)
  • compressing 2nvh-2019.may15.e49.mrc (Wed May 15 13:53:32 2019)
  • FINISHED (Wed May 15 13:53:32 2019)

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Log file display

Show last lines of log file 
Terminal display
		
Message: completed conversion of PDB file: 2nvh-2019.may15.e49.pdb (size: 38k) 
Message: converted 1224 atoms of 1224 atoms 
Message: found 1224 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/may15/e49/2nvh-2019.may15.e49.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 2nvh-2019.may15.e49.obj 
Message: UCSF Chimera completed in 7.08 sec 
OBJFILE /var/www/html/3vee/output/2019/may15/e49/2nvh-2019.may15.e49.obj.gz 
Message: analyzing volume 
Message: normal CoM (1.0, -4.8, -7.4) Å 
Message: reduced center failed 
Message: volume analysis completed in 0.88 sec 
Message: compressing 2nvh-2019.may15.e49.pdb 
Message: compressing 2nvh-2019.may15.e49.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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