3v Running Log for JobId '2018.dec06.1c6'

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  • host ip address=196.251.14.194 (Thu Dec 6 12:42:26 2018)
  • converting pdb into xyzr (Thu Dec 6 12:42:26 2018)
  • completed conversion of PDB file: 2018.dec06.1c6.pdb (size: 1025k) (Thu Dec 6 12:42:39 2018)
  • converted 32798 atoms of 32798 atoms (Thu Dec 6 12:42:39 2018)
  • found 32798 atoms in pdb (Thu Dec 6 12:42:39 2018)
  • running 3v volume program (Thu Dec 6 12:42:39 2018)
  • smoothing out volume (Thu Dec 6 12:42:40 2018)
  • imaging volume (download mrc) with UCSF Chimera (Thu Dec 6 12:42:40 2018)
  • UCSF Chimera created Jmol compatible file (Thu Dec 6 12:42:52 2018)
  • compressing 2018.dec06.1c6.obj (Thu Dec 6 12:42:52 2018)
  • UCSF Chimera completed in 12.67 sec (Thu Dec 6 12:42:52 2018)
  • analyzing volume (Thu Dec 6 12:42:52 2018)
  • normal CoM (-22.0, -2.0, 18.0) Å (Thu Dec 6 12:42:58 2018)
  • reduced center failed (Thu Dec 6 12:42:59 2018)
  • volume analysis completed in 6.82 sec (Thu Dec 6 12:42:59 2018)
  • compressing 2018.dec06.1c6.mrc (Thu Dec 6 12:42:59 2018)
  • FINISHED (Thu Dec 6 12:42:59 2018)

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Log file display

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Terminal display
		
/srv/output/2018/dec06/1c6 
Message: completed conversion of PDB file: 2018.dec06.1c6.pdb (size: 1025k) 
Message: converted 32798 atoms of 32798 atoms 
Message: found 32798 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2018/dec06/1c6/2018.dec06.1c6.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.dec06.1c6.obj 
Message: UCSF Chimera completed in 12.67 sec 
OBJFILE /var/www/html/3vee/output/2018/dec06/1c6/2018.dec06.1c6.obj.gz 
Message: analyzing volume 
Message: normal CoM (-22.0, -2.0, 18.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 6.82 sec 
Message: compressing 2018.dec06.1c6.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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