3v Running Log for JobId '2017.aug11.799'

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  • host ip address=117.201.233.16 (Fri Aug 11 22:26:13 2017)
  • converting pdb into xyzr (Fri Aug 11 22:26:14 2017)
  • completed conversion of PDB file: 2017.aug11.799.pdb (size: 224k) (Fri Aug 11 22:26:16 2017)
  • converted 7171 atoms of 7171 atoms (Fri Aug 11 22:26:16 2017)
  • found 7171 atoms in pdb (Fri Aug 11 22:26:16 2017)
  • running 3v volume program (Fri Aug 11 22:26:16 2017)
  • smoothing out volume (Fri Aug 11 22:26:17 2017)
  • imaging volume (download mrc) with UCSF Chimera (Fri Aug 11 22:26:17 2017)
  • UCSF Chimera created Jmol compatible file (Fri Aug 11 22:26:27 2017)
  • compressing 2017.aug11.799.obj (Fri Aug 11 22:26:27 2017)
  • UCSF Chimera completed in 10.78 sec (Fri Aug 11 22:26:28 2017)
  • analyzing volume (Fri Aug 11 22:26:28 2017)
  • normal CoM (-24.0, 1.0, 24.1) Å (Fri Aug 11 22:26:39 2017)
  • reduced center failed (Fri Aug 11 22:26:42 2017)
  • volume analysis completed in 14.38 sec (Fri Aug 11 22:26:42 2017)
  • compressing 2017.aug11.799.mrc (Fri Aug 11 22:26:42 2017)
  • FINISHED (Fri Aug 11 22:26:43 2017)

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Log file display

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Terminal display
		
/var/www/html/output/2017/aug11/799 
Message: completed conversion of PDB file: 2017.aug11.799.pdb (size: 224k) 
Message: converted 7171 atoms of 7171 atoms 
Message: found 7171 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2017/aug11/799/2017.aug11.799.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.aug11.799.obj 
Message: UCSF Chimera completed in 10.78 sec 
OBJFILE /var/www/html/3vee/output/2017/aug11/799/2017.aug11.799.obj.gz 
Message: analyzing volume 
Message: normal CoM (-24.0, 1.0, 24.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 14.38 sec 
Message: compressing 2017.aug11.799.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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