3v Running Log for JobId '2018.apr16.709'

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  • host ip address=147.122.46.35 (Mon Apr 16 08:58:29 2018)
  • converting pdb into xyzr (Mon Apr 16 08:58:29 2018)
  • completed conversion of PDB file: 2018.apr16.709.pdb (size: 102k) (Mon Apr 16 08:58:30 2018)
  • converted 3256 atoms of 3256 atoms (Mon Apr 16 08:58:30 2018)
  • found 3256 atoms in pdb (Mon Apr 16 08:58:30 2018)
  • running 3v solvent program (Mon Apr 16 08:58:30 2018)
  • imaging volume (download mrc) with UCSF Chimera (Mon Apr 16 08:58:39 2018)
  • UCSF Chimera created Jmol compatible file (Mon Apr 16 08:58:44 2018)
  • compressing 2018.apr16.709.obj (Mon Apr 16 08:58:44 2018)
  • UCSF Chimera completed in 5.51 sec (Mon Apr 16 08:58:45 2018)
  • analyzing volume (Mon Apr 16 08:58:45 2018)
  • normal CoM (-24.8, 5.9, 4.5) Å (Mon Apr 16 08:58:56 2018)
  • reduced center failed (Mon Apr 16 08:58:57 2018)
  • volume analysis completed in 12.59 sec (Mon Apr 16 08:58:57 2018)
  • compressing 2018.apr16.709.mrc (Mon Apr 16 08:58:57 2018)
  • FINISHED (Mon Apr 16 08:58:58 2018)

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Log file display

Show last lines of log file 
Terminal display
		
Message: converting pdb into xyzr 
/var/www/html/output/2018/apr16/709 
Message: completed conversion of PDB file: 2018.apr16.709.pdb (size: 102k) 
Message: converted 3256 atoms of 3256 atoms 
Message: found 3256 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2018/apr16/709/2018.apr16.709.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2018.apr16.709.obj 
Message: UCSF Chimera completed in 5.51 sec 
OBJFILE /var/www/html/3vee/output/2018/apr16/709/2018.apr16.709.obj.gz 
Message: analyzing volume 
Message: normal CoM (-24.8, 5.9, 4.5) Å 
Message: reduced center failed 
Message: volume analysis completed in 12.59 sec 
Message: compressing 2018.apr16.709.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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