3v Running Log for JobId '2019.feb04.8b2'

Program is still running, progress is shown below

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  • host ip address=141.106.168.92 (Mon Feb 4 18:03:47 2019)
  • converting pdb into xyzr (Mon Feb 4 18:03:47 2019)
  • completed conversion of PDB file: 2019.feb04.8b2.pdb (size: 60k) (Mon Feb 4 18:03:48 2019)
  • converted 1926 atoms of 1926 atoms (Mon Feb 4 18:03:48 2019)
  • found 1926 atoms in pdb (Mon Feb 4 18:03:48 2019)
  • running 3v solvent program (Mon Feb 4 18:03:48 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Feb 4 18:03:57 2019)
  • UCSF Chimera created Jmol compatible file (Mon Feb 4 18:04:03 2019)
  • compressing 2019.feb04.8b2.obj (Mon Feb 4 18:04:03 2019)
  • UCSF Chimera completed in 5.61 sec (Mon Feb 4 18:04:03 2019)
  • analyzing volume (Mon Feb 4 18:04:03 2019)
  • normal CoM (-19.8, -10.6, -8.6) Å (Mon Feb 4 18:04:15 2019)
  • reduced center failed (Mon Feb 4 18:04:17 2019)
  • volume analysis completed in 13.73 sec (Mon Feb 4 18:04:17 2019)
  • compressing 2019.feb04.8b2.mrc (Mon Feb 4 18:04:17 2019)
  • FINISHED (Mon Feb 4 18:04:17 2019)

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Log file display

Show last lines of log file 
Terminal display
		
Message: converting pdb into xyzr 
/srv/output/2019/feb04/8b2 
Message: completed conversion of PDB file: 2019.feb04.8b2.pdb (size: 60k) 
Message: converted 1926 atoms of 1926 atoms 
Message: found 1926 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2019/feb04/8b2/2019.feb04.8b2.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2019.feb04.8b2.obj 
Message: UCSF Chimera completed in 5.61 sec 
OBJFILE /var/www/html/3vee/output/2019/feb04/8b2/2019.feb04.8b2.obj.gz 
Message: analyzing volume 
Message: normal CoM (-19.8, -10.6, -8.6) Å 
Message: reduced center failed 
Message: volume analysis completed in 13.73 sec 
Message: compressing 2019.feb04.8b2.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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