3v Running Log for JobId '2017.mar13.863'

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  • host ip address=141.2.132.87 (Mon Mar 13 05:43:56 2017)
  • converting pdb into xyzr (Mon Mar 13 05:43:56 2017)
  • completed conversion of PDB file: 2017.mar13.863.pdb (size: 69k) (Mon Mar 13 05:43:57 2017)
  • converted 2212 atoms of 2212 atoms (Mon Mar 13 05:43:57 2017)
  • found 2212 atoms in pdb (Mon Mar 13 05:43:57 2017)
  • running 3v volume program (Mon Mar 13 05:43:57 2017)
  • smoothing out volume (Mon Mar 13 05:43:57 2017)
  • imaging volume (download mrc) with UCSF Chimera (Mon Mar 13 05:43:57 2017)
  • UCSF Chimera created Jmol compatible file (Mon Mar 13 05:44:08 2017)
  • compressing 2017.mar13.863.obj (Mon Mar 13 05:44:08 2017)
  • UCSF Chimera completed in 10.83 sec (Mon Mar 13 05:44:08 2017)
  • analyzing volume (Mon Mar 13 05:44:08 2017)
  • normal CoM (4.6, -1.4, -4.6) Å (Mon Mar 13 05:44:10 2017)
  • reduced center failed (Mon Mar 13 05:44:10 2017)
  • volume analysis completed in 1.64 sec (Mon Mar 13 05:44:10 2017)
  • compressing 2017.mar13.863.mrc (Mon Mar 13 05:44:10 2017)
  • FINISHED (Mon Mar 13 05:44:10 2017)

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Log file display

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Terminal display
		
/var/www/html/output/2017/mar13/863 
Message: completed conversion of PDB file: 2017.mar13.863.pdb (size: 69k) 
Message: converted 2212 atoms of 2212 atoms 
Message: found 2212 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2017/mar13/863/2017.mar13.863.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 2017.mar13.863.obj 
Message: UCSF Chimera completed in 10.83 sec 
OBJFILE /var/www/html/3vee/output/2017/mar13/863/2017.mar13.863.obj.gz 
Message: analyzing volume 
Message: normal CoM (4.6, -1.4, -4.6) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.64 sec 
Message: compressing 2017.mar13.863.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] yahoo.com>
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