3v Running Log for JobId '2018.may16.af5'

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  • host ip address=137.158.34.34 (Wed May 16 09:45:58 2018)
  • converting pdb into xyzr (Wed May 16 09:45:58 2018)
  • completed conversion of PDB file: 2018.may16.af5.pdb (size: 11k) (Wed May 16 09:45:58 2018)
  • converted 336 atoms of 336 atoms (Wed May 16 09:45:58 2018)
  • found 336 atoms in pdb (Wed May 16 09:45:58 2018)
  • running 3v volume program (Wed May 16 09:45:58 2018)
  • smoothing out volume (Wed May 16 09:45:58 2018)
  • imaging volume (download mrc) with UCSF Chimera (Wed May 16 09:45:58 2018)
  • UCSF Chimera created Jmol compatible file (Wed May 16 09:46:05 2018)
  • compressing 2018.may16.af5.obj (Wed May 16 09:46:05 2018)
  • UCSF Chimera completed in 7.31 sec (Wed May 16 09:46:06 2018)
  • analyzing volume (Wed May 16 09:46:06 2018)
  • normal CoM (0.4, -0.8, -3.5) Å (Wed May 16 09:46:06 2018)
  • reduced center failed (Wed May 16 09:46:06 2018)
  • volume analysis completed in 0.89 sec (Wed May 16 09:46:06 2018)
  • compressing 2018.may16.af5.mrc (Wed May 16 09:46:06 2018)
  • FINISHED (Wed May 16 09:46:07 2018)

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Log file display

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Terminal display
		
/var/www/html/output/2018/may16/af5 
Message: completed conversion of PDB file: 2018.may16.af5.pdb (size: 11k) 
Message: converted 336 atoms of 336 atoms 
Message: found 336 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2018/may16/af5/2018.may16.af5.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.may16.af5.obj 
Message: UCSF Chimera completed in 7.31 sec 
OBJFILE /var/www/html/3vee/output/2018/may16/af5/2018.may16.af5.obj.gz 
Message: analyzing volume 
Message: normal CoM (0.4, -0.8, -3.5) Å 
Message: reduced center failed 
Message: volume analysis completed in 0.89 sec 
Message: compressing 2018.may16.af5.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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