3v Running Log for JobId '2019.sep11.f62'

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  • host ip address=149.156.87.113 (Wed Sep 11 11:03:36 2019)
  • converting pdb into xyzr (Wed Sep 11 11:03:36 2019)
  • completed conversion of PDB file: 2019.sep11.f62.pdb (size: 1k) (Wed Sep 11 11:03:36 2019)
  • converted 24 atoms of 24 atoms (Wed Sep 11 11:03:36 2019)
  • found 24 atoms in pdb (Wed Sep 11 11:03:36 2019)
  • running 3v volume program (Wed Sep 11 11:03:36 2019)
  • smoothing out volume (Wed Sep 11 11:03:36 2019)
  • imaging volume (download mrc) with UCSF Chimera (Wed Sep 11 11:03:36 2019)
  • UCSF Chimera created Jmol compatible file (Wed Sep 11 11:03:42 2019)
  • compressing 2019.sep11.f62.obj (Wed Sep 11 11:03:42 2019)
  • UCSF Chimera completed in 6.17 sec (Wed Sep 11 11:03:42 2019)
  • analyzing volume (Wed Sep 11 11:03:42 2019)
  • normal CoM (-1.0, -0.3, -1.6) Å (Wed Sep 11 11:03:42 2019)
  • reduced center failed (Wed Sep 11 11:03:42 2019)
  • volume analysis completed in 135.9 msec (Wed Sep 11 11:03:42 2019)
  • compressing 2019.sep11.f62.mrc (Wed Sep 11 11:03:42 2019)
  • FINISHED (Wed Sep 11 11:03:42 2019)

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Log file display

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Terminal display
		
/srv/output/2019/sep11/f62 
Message: completed conversion of PDB file: 2019.sep11.f62.pdb (size: 1k) 
Message: converted 24 atoms of 24 atoms 
Message: found 24 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/sep11/f62/2019.sep11.f62.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.sep11.f62.obj 
Message: UCSF Chimera completed in 6.17 sec 
OBJFILE /var/www/html/3vee/output/2019/sep11/f62/2019.sep11.f62.obj.gz 
Message: analyzing volume 
Message: normal CoM (-1.0, -0.3, -1.6) Å 
Message: reduced center failed 
Message: volume analysis completed in 135.9 msec 
Message: compressing 2019.sep11.f62.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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