3v Running Log for JobId '2018.apr16.918'

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  • host ip address=131.169.131.156 (Mon Apr 16 09:36:44 2018)
  • converting pdb into xyzr (Mon Apr 16 09:36:45 2018)
  • completed conversion of PDB file: 2018.apr16.918.pdb (size: 2k) (Mon Apr 16 09:36:45 2018)
  • converted 60 atoms of 60 atoms (Mon Apr 16 09:36:45 2018)
  • found 60 atoms in pdb (Mon Apr 16 09:36:45 2018)
  • running 3v volume program (Mon Apr 16 09:36:45 2018)
  • smoothing out volume (Mon Apr 16 09:36:45 2018)
  • imaging volume (download mrc) with UCSF Chimera (Mon Apr 16 09:36:45 2018)
  • UCSF Chimera created Jmol compatible file (Mon Apr 16 09:36:54 2018)
  • compressing 2018.apr16.918.obj (Mon Apr 16 09:36:54 2018)
  • UCSF Chimera completed in 8.97 sec (Mon Apr 16 09:36:54 2018)
  • analyzing volume (Mon Apr 16 09:36:54 2018)
  • normal CoM (-1.0, -1.0, -1.0) Å (Mon Apr 16 09:36:54 2018)
  • reduced center failed (Mon Apr 16 09:36:54 2018)
  • volume analysis completed in 267.41 msec (Mon Apr 16 09:36:54 2018)
  • compressing 2018.apr16.918.mrc (Mon Apr 16 09:36:54 2018)
  • FINISHED (Mon Apr 16 09:36:54 2018)

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Log file display

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Terminal display
		
/var/www/html/output/2018/apr16/918 
Message: completed conversion of PDB file: 2018.apr16.918.pdb (size: 2k) 
Message: converted 60 atoms of 60 atoms 
Message: found 60 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2018/apr16/918/2018.apr16.918.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 2018.apr16.918.obj 
Message: UCSF Chimera completed in 8.97 sec 
OBJFILE /var/www/html/3vee/output/2018/apr16/918/2018.apr16.918.obj.gz 
Message: analyzing volume 
Message: normal CoM (-1.0, -1.0, -1.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 267.41 msec 
Message: compressing 2018.apr16.918.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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