3v Running Log for JobId '2019.feb10.876'

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  • host ip address=82.9.236.83 (Sun Feb 10 17:44:49 2019)
  • converting pdb into xyzr (Sun Feb 10 17:44:49 2019)
  • completed conversion of PDB file: 2019.feb10.876.pdb (size: 94k) (Sun Feb 10 17:44:51 2019)
  • converted 2998 atoms of 2998 atoms (Sun Feb 10 17:44:51 2019)
  • found 2998 atoms in pdb (Sun Feb 10 17:44:51 2019)
  • running 3v volume program (Sun Feb 10 17:44:51 2019)
  • smoothing out volume (Sun Feb 10 17:44:52 2019)
  • imaging volume (download mrc) with UCSF Chimera (Sun Feb 10 17:44:52 2019)
  • UCSF Chimera created Jmol compatible file (Sun Feb 10 17:45:03 2019)
  • compressing 2019.feb10.876.obj (Sun Feb 10 17:45:03 2019)
  • UCSF Chimera completed in 11.78 sec (Sun Feb 10 17:45:04 2019)
  • analyzing volume (Sun Feb 10 17:45:04 2019)
  • normal CoM (0.3, -1.5, -0.6) Å (Sun Feb 10 17:45:14 2019)
  • reduced center failed (Sun Feb 10 17:45:16 2019)
  • volume analysis completed in 12.53 sec (Sun Feb 10 17:45:16 2019)
  • compressing 2019.feb10.876.pdb (Sun Feb 10 17:45:16 2019)
  • compressing 2019.feb10.876.mrc (Sun Feb 10 17:45:18 2019)
  • FINISHED (Sun Feb 10 17:45:19 2019)

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Log file display

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Terminal display
		
Message: completed conversion of PDB file: 2019.feb10.876.pdb (size: 94k) 
Message: converted 2998 atoms of 2998 atoms 
Message: found 2998 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/feb10/876/2019.feb10.876.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 2019.feb10.876.obj 
Message: UCSF Chimera completed in 11.78 sec 
OBJFILE /var/www/html/3vee/output/2019/feb10/876/2019.feb10.876.obj.gz 
Message: analyzing volume 
Message: normal CoM (0.3, -1.5, -0.6) Å 
Message: reduced center failed 
Message: volume analysis completed in 12.53 sec 
Message: compressing 2019.feb10.876.pdb 
Message: compressing 2019.feb10.876.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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