3v Running Log for JobId '2018.dec05.d3d'

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  • host ip address=85.139.158.100 (Wed Dec 5 17:50:26 2018)
  • converting pdb into xyzr (Wed Dec 5 17:50:26 2018)
  • completed conversion of PDB file: 2018.dec05.d3d.pdb (size: 59k) (Wed Dec 5 17:50:27 2018)
  • converted 1896 atoms of 1896 atoms (Wed Dec 5 17:50:27 2018)
  • found 1896 atoms in pdb (Wed Dec 5 17:50:27 2018)
  • running 3v volume program (Wed Dec 5 17:50:27 2018)
  • smoothing out volume (Wed Dec 5 17:50:28 2018)
  • imaging volume (download mrc) with UCSF Chimera (Wed Dec 5 17:50:28 2018)
  • UCSF Chimera created Jmol compatible file (Wed Dec 5 17:50:34 2018)
  • compressing 2018.dec05.d3d.obj (Wed Dec 5 17:50:34 2018)
  • UCSF Chimera completed in 7.19 sec (Wed Dec 5 17:50:35 2018)
  • analyzing volume (Wed Dec 5 17:50:35 2018)
  • normal CoM (-79.5, 1.6, 80.8) Å (Wed Dec 5 17:51:05 2018)
  • reduced center failed (Wed Dec 5 17:51:10 2018)
  • volume analysis completed in 35.39 sec (Wed Dec 5 17:51:10 2018)
  • compressing 2018.dec05.d3d.mrc (Wed Dec 5 17:51:10 2018)
  • FINISHED (Wed Dec 5 17:51:11 2018)

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Log file display

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Terminal display
		
/srv/output/2018/dec05/d3d 
Message: completed conversion of PDB file: 2018.dec05.d3d.pdb (size: 59k) 
Message: converted 1896 atoms of 1896 atoms 
Message: found 1896 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2018/dec05/d3d/2018.dec05.d3d.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.dec05.d3d.obj 
Message: UCSF Chimera completed in 7.19 sec 
OBJFILE /var/www/html/3vee/output/2018/dec05/d3d/2018.dec05.d3d.obj.gz 
Message: analyzing volume 
Message: normal CoM (-79.5, 1.6, 80.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 35.39 sec 
Message: compressing 2018.dec05.d3d.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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