3v Running Log for JobId '2020.feb12.22a'

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  • host ip address=64.54.0.187 (Wed Feb 12 22:56:21 2020)
  • downloading pdb file (Wed Feb 12 22:56:21 2020)
  • failed to download pdb id: 2kqt (Wed Feb 12 22:56:21 2020)
  • trying download pdb id again without bio unit (Wed Feb 12 22:56:23 2020)
  • completed download of PDB id 2kqt (size: 2244 k, 28372 lines) (Wed Feb 12 22:56:23 2020)
  • converting pdb into xyzr (Wed Feb 12 22:56:23 2020)
  • completed conversion of PDB file: 2kqt-2020.feb12.22a.pdb (size: 856k) (Wed Feb 12 22:56:33 2020)
  • converted 27404 atoms of 27404 atoms (Wed Feb 12 22:56:33 2020)
  • found 27404 atoms in pdb (Wed Feb 12 22:56:33 2020)
  • running 3v volume program (Wed Feb 12 22:56:33 2020)
  • smoothing out volume (Wed Feb 12 22:56:34 2020)
  • imaging volume (download mrc) with UCSF Chimera (Wed Feb 12 22:56:34 2020)
  • UCSF Chimera created Jmol compatible file (Wed Feb 12 22:56:41 2020)
  • compressing 2kqt-2020.feb12.22a.obj (Wed Feb 12 22:56:41 2020)
  • UCSF Chimera completed in 7.45 sec (Wed Feb 12 22:56:41 2020)
  • analyzing volume (Wed Feb 12 22:56:41 2020)
  • normal CoM (0.9, -2.0, -6.0) Å (Wed Feb 12 22:56:42 2020)
  • reduced center failed (Wed Feb 12 22:56:42 2020)
  • volume analysis completed in 0.55 sec (Wed Feb 12 22:56:42 2020)
  • compressing 2kqt-2020.feb12.22a.mrc (Wed Feb 12 22:56:42 2020)
  • FINISHED (Wed Feb 12 22:56:42 2020)

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Log file display

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Terminal display
		
/srv/output/2020/feb12/22a 
Message: completed conversion of PDB file: 2kqt-2020.feb12.22a.pdb (size: 856k) 
Message: converted 27404 atoms of 27404 atoms 
Message: found 27404 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2020/feb12/22a/2kqt-2020.feb12.22a.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 2kqt-2020.feb12.22a.obj 
Message: UCSF Chimera completed in 7.45 sec 
OBJFILE /var/www/html/3vee/output/2020/feb12/22a/2kqt-2020.feb12.22a.obj.gz 
Message: analyzing volume 
Message: normal CoM (0.9, -2.0, -6.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 0.55 sec 
Message: compressing 2kqt-2020.feb12.22a.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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