3v Running Log for JobId '2018.apr16.ec4'

Program is still running, progress is shown below

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  • host ip address=147.122.46.35 (Mon Apr 16 08:55:49 2018)
  • converting pdb into xyzr (Mon Apr 16 08:55:49 2018)
  • completed conversion of PDB file: 2018.apr16.ec4.pdb (size: 101k) (Mon Apr 16 08:55:50 2018)
  • converted 3231 atoms of 3231 atoms (Mon Apr 16 08:55:50 2018)
  • found 3231 atoms in pdb (Mon Apr 16 08:55:50 2018)
  • running 3v solvent program (Mon Apr 16 08:55:50 2018)
  • imaging volume (download mrc) with UCSF Chimera (Mon Apr 16 08:56:00 2018)
  • UCSF Chimera created Jmol compatible file (Mon Apr 16 08:56:06 2018)
  • compressing 2018.apr16.ec4.obj (Mon Apr 16 08:56:06 2018)
  • UCSF Chimera completed in 6.91 sec (Mon Apr 16 08:56:07 2018)
  • analyzing volume (Mon Apr 16 08:56:07 2018)
  • normal CoM (-19.6, -0.5, 11.8) Å (Mon Apr 16 08:56:14 2018)
  • reduced center failed (Mon Apr 16 08:56:20 2018)
  • volume analysis completed in 13.35 sec (Mon Apr 16 08:56:20 2018)
  • compressing 2018.apr16.ec4.mrc (Mon Apr 16 08:56:20 2018)
  • FINISHED (Mon Apr 16 08:56:20 2018)

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Log file display

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Terminal display
		
Message: converting pdb into xyzr 
/var/www/html/output/2018/apr16/ec4 
Message: completed conversion of PDB file: 2018.apr16.ec4.pdb (size: 101k) 
Message: converted 3231 atoms of 3231 atoms 
Message: found 3231 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2018/apr16/ec4/2018.apr16.ec4.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2018.apr16.ec4.obj 
Message: UCSF Chimera completed in 6.91 sec 
OBJFILE /var/www/html/3vee/output/2018/apr16/ec4/2018.apr16.ec4.obj.gz 
Message: analyzing volume 
Message: normal CoM (-19.6, -0.5, 11.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 13.35 sec 
Message: compressing 2018.apr16.ec4.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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