3v Running Log for JobId '2020.may21.b6f'

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  • host ip address=50.209.85.210 (Thu May 21 22:21:48 2020)
  • converting pdb into xyzr (Thu May 21 22:21:49 2020)
  • completed conversion of PDB file: 2020.may21.b6f.pdb (size: 188k) (Thu May 21 22:21:51 2020)
  • converted 6016 atoms of 6016 atoms (Thu May 21 22:21:51 2020)
  • found 6016 atoms in pdb (Thu May 21 22:21:51 2020)
  • running 3v volume program (Thu May 21 22:21:51 2020)
  • smoothing out volume (Thu May 21 22:21:51 2020)
  • imaging volume (download mrc) with UCSF Chimera (Thu May 21 22:21:51 2020)
  • UCSF Chimera created Jmol compatible file (Thu May 21 22:22:00 2020)
  • compressing 2020.may21.b6f.obj (Thu May 21 22:22:00 2020)
  • UCSF Chimera completed in 8.81 sec (Thu May 21 22:22:00 2020)
  • analyzing volume (Thu May 21 22:22:00 2020)
  • normal CoM (9.7, -0.7, -15.4) Å (Thu May 21 22:22:02 2020)
  • reduced center failed (Thu May 21 22:22:02 2020)
  • volume analysis completed in 1.86 sec (Thu May 21 22:22:02 2020)
  • compressing 2020.may21.b6f.mrc (Thu May 21 22:22:02 2020)
  • FINISHED (Thu May 21 22:22:02 2020)

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Log file display

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Terminal display
		
/srv/output/2020/may21/b6f 
Message: completed conversion of PDB file: 2020.may21.b6f.pdb (size: 188k) 
Message: converted 6016 atoms of 6016 atoms 
Message: found 6016 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2020/may21/b6f/2020.may21.b6f.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 2020.may21.b6f.obj 
Message: UCSF Chimera completed in 8.81 sec 
OBJFILE /var/www/html/3vee/output/2020/may21/b6f/2020.may21.b6f.obj.gz 
Message: analyzing volume 
Message: normal CoM (9.7, -0.7, -15.4) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.86 sec 
Message: compressing 2020.may21.b6f.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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