3v Running Log for JobId '2018.mar13.2bf'

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  • host ip address=146.107.104.133 (Tue Mar 13 11:33:09 2018)
  • converting pdb into xyzr (Tue Mar 13 11:33:09 2018)
  • completed conversion of PDB file: 2018.mar13.2bf.pdb (size: 64k) (Tue Mar 13 11:33:10 2018)
  • converted 2054 atoms of 2054 atoms (Tue Mar 13 11:33:10 2018)
  • found 2054 atoms in pdb (Tue Mar 13 11:33:10 2018)
  • running 3v volume program (Tue Mar 13 11:33:10 2018)
  • smoothing out volume (Tue Mar 13 11:33:11 2018)
  • imaging volume (download mrc) with UCSF Chimera (Tue Mar 13 11:33:11 2018)
  • UCSF Chimera created Jmol compatible file (Tue Mar 13 11:33:18 2018)
  • compressing 2018.mar13.2bf.obj (Tue Mar 13 11:33:18 2018)
  • UCSF Chimera completed in 7.43 sec (Tue Mar 13 11:33:18 2018)
  • analyzing volume (Tue Mar 13 11:33:18 2018)
  • normal CoM (5.5, -1.0, -11.1) Å (Tue Mar 13 11:33:19 2018)
  • reduced center failed (Tue Mar 13 11:33:19 2018)
  • volume analysis completed in 1.42 sec (Tue Mar 13 11:33:19 2018)
  • compressing 2018.mar13.2bf.mrc (Tue Mar 13 11:33:19 2018)
  • FINISHED (Tue Mar 13 11:33:19 2018)

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Log file display

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Terminal display
		
/var/www/html/output/2018/mar13/2bf 
Message: completed conversion of PDB file: 2018.mar13.2bf.pdb (size: 64k) 
Message: converted 2054 atoms of 2054 atoms 
Message: found 2054 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2018/mar13/2bf/2018.mar13.2bf.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.mar13.2bf.obj 
Message: UCSF Chimera completed in 7.43 sec 
OBJFILE /var/www/html/3vee/output/2018/mar13/2bf/2018.mar13.2bf.obj.gz 
Message: analyzing volume 
Message: normal CoM (5.5, -1.0, -11.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.42 sec 
Message: compressing 2018.mar13.2bf.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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