3v Running Log for JobId '2018.mar13.d39'

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  • host ip address=130.208.167.196 (Tue Mar 13 10:42:09 2018)
  • converting pdb into xyzr (Tue Mar 13 10:42:09 2018)
  • completed conversion of PDB file: 2018.mar13.d39.pdb (size: 252k) (Tue Mar 13 10:42:15 2018)
  • converted 8069 atoms of 8069 atoms (Tue Mar 13 10:42:15 2018)
  • found 8069 atoms in pdb (Tue Mar 13 10:42:15 2018)
  • running 3v volume program (Tue Mar 13 10:42:15 2018)
  • smoothing out volume (Tue Mar 13 10:42:15 2018)
  • imaging volume (download mrc) with UCSF Chimera (Tue Mar 13 10:42:15 2018)
  • UCSF Chimera created Jmol compatible file (Tue Mar 13 10:42:25 2018)
  • compressing 2018.mar13.d39.obj (Tue Mar 13 10:42:25 2018)
  • UCSF Chimera completed in 10.39 sec (Tue Mar 13 10:42:26 2018)
  • analyzing volume (Tue Mar 13 10:42:26 2018)
  • normal CoM (-3.2, 0.1, -3.1) Å (Tue Mar 13 10:42:29 2018)
  • reduced center failed (Tue Mar 13 10:42:30 2018)
  • volume analysis completed in 4.75 sec (Tue Mar 13 10:42:30 2018)
  • compressing 2018.mar13.d39.mrc (Tue Mar 13 10:42:30 2018)
  • FINISHED (Tue Mar 13 10:42:31 2018)

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Log file display

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Terminal display
		
/var/www/html/output/2018/mar13/d39 
Message: completed conversion of PDB file: 2018.mar13.d39.pdb (size: 252k) 
Message: converted 8069 atoms of 8069 atoms 
Message: found 8069 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2018/mar13/d39/2018.mar13.d39.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.d39.obj 
Message: UCSF Chimera completed in 10.39 sec 
OBJFILE /var/www/html/3vee/output/2018/mar13/d39/2018.mar13.d39.obj.gz 
Message: analyzing volume 
Message: normal CoM (-3.2, 0.1, -3.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 4.75 sec 
Message: compressing 2018.mar13.d39.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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