3v Running Log for JobId '2018.jan07.01b'

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  • host ip address=37.170.63.99 (Sun Jan 7 10:22:35 2018)
  • converting pdb into xyzr (Sun Jan 7 10:22:35 2018)
  • completed conversion of PDB file: 2018.jan07.01b.pdb (size: 119k) (Sun Jan 7 10:22:36 2018)
  • converted 3793 atoms of 3793 atoms (Sun Jan 7 10:22:36 2018)
  • found 3793 atoms in pdb (Sun Jan 7 10:22:36 2018)
  • running 3v volume program (Sun Jan 7 10:22:36 2018)
  • smoothing out volume (Sun Jan 7 10:22:37 2018)
  • imaging volume (download mrc) with UCSF Chimera (Sun Jan 7 10:22:37 2018)
  • UCSF Chimera created Jmol compatible file (Sun Jan 7 10:22:44 2018)
  • compressing 2018.jan07.01b.obj (Sun Jan 7 10:22:44 2018)
  • UCSF Chimera completed in 7.37 sec (Sun Jan 7 10:22:44 2018)
  • analyzing volume (Sun Jan 7 10:22:44 2018)
  • normal CoM (-1.4, -2.1, 1.9) Å (Sun Jan 7 10:22:45 2018)
  • reduced center failed (Sun Jan 7 10:22:45 2018)
  • volume analysis completed in 1.3 sec (Sun Jan 7 10:22:45 2018)
  • compressing 2018.jan07.01b.mrc (Sun Jan 7 10:22:45 2018)
  • FINISHED (Sun Jan 7 10:22:45 2018)

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Log file display

Show last lines of log file 
Terminal display
		
/var/www/html/output/2018/jan07/01b 
Message: completed conversion of PDB file: 2018.jan07.01b.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/jan07/01b/2018.jan07.01b.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.jan07.01b.obj 
Message: UCSF Chimera completed in 7.37 sec 
OBJFILE /var/www/html/3vee/output/2018/jan07/01b/2018.jan07.01b.obj.gz 
Message: analyzing volume 
Message: normal CoM (-1.4, -2.1, 1.9) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.3 sec 
Message: compressing 2018.jan07.01b.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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If you find this useful or want more functionality please contact Neil <vossman77 [at] gmail [dot] com>
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