3v Running Log for JobId '2018.nov07.6da'

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  • host ip address=78.226.184.88 (Wed Nov 7 14:02:26 2018)
  • downloading pdb file (Wed Nov 7 14:02:26 2018)
  • failed to download pdb id: 3lvm (Wed Nov 7 14:02:26 2018)
  • trying download pdb id again without bio unit (Wed Nov 7 14:02:28 2018)
  • completed download of PDB id 3lvm (size: 570 k, 7211 lines) (Wed Nov 7 14:02:28 2018)
  • converting pdb into xyzr (Wed Nov 7 14:02:28 2018)
  • completed conversion of PDB file: 3lvm-2018.nov07.6da.pdb (size: 192k) (Wed Nov 7 14:02:33 2018)
  • converted 6155 atoms of 6155 atoms (Wed Nov 7 14:02:33 2018)
  • found 6155 atoms in pdb (Wed Nov 7 14:02:33 2018)
  • running 3v volume program (Wed Nov 7 14:02:33 2018)
  • smoothing out volume (Wed Nov 7 14:02:33 2018)
  • imaging volume (download mrc) with UCSF Chimera (Wed Nov 7 14:02:33 2018)
  • UCSF Chimera created Jmol compatible file (Wed Nov 7 14:02:40 2018)
  • compressing 3lvm-2018.nov07.6da.obj (Wed Nov 7 14:02:40 2018)
  • UCSF Chimera completed in 7.42 sec (Wed Nov 7 14:02:41 2018)
  • analyzing volume (Wed Nov 7 14:02:41 2018)
  • normal CoM (-15.3, -0.0, 14.6) Å (Wed Nov 7 14:02:44 2018)
  • reduced center failed (Wed Nov 7 14:02:44 2018)
  • volume analysis completed in 3.84 sec (Wed Nov 7 14:02:44 2018)
  • compressing 3lvm-2018.nov07.6da.mrc (Wed Nov 7 14:02:44 2018)
  • FINISHED (Wed Nov 7 14:02:45 2018)

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Log file display

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Terminal display
		
/srv/output/2018/nov07/6da 
Message: completed conversion of PDB file: 3lvm-2018.nov07.6da.pdb (size: 192k) 
Message: converted 6155 atoms of 6155 atoms 
Message: found 6155 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2018/nov07/6da/3lvm-2018.nov07.6da.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 3lvm-2018.nov07.6da.obj 
Message: UCSF Chimera completed in 7.42 sec 
OBJFILE /var/www/html/3vee/output/2018/nov07/6da/3lvm-2018.nov07.6da.obj.gz 
Message: analyzing volume 
Message: normal CoM (-15.3, -0.0, 14.6) Å 
Message: reduced center failed 
Message: volume analysis completed in 3.84 sec 
Message: compressing 3lvm-2018.nov07.6da.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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