3v Running Log for JobId '2020.feb12.122'

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  • host ip address=124.16.180.100 (Wed Feb 12 13:21:58 2020)
  • converting pdb into xyzr (Wed Feb 12 13:21:58 2020)
  • completed conversion of PDB file: 2020.feb12.122.pdb (size: 50k) (Wed Feb 12 13:22:00 2020)
  • converted 1598 atoms of 1598 atoms (Wed Feb 12 13:22:00 2020)
  • found 1598 atoms in pdb (Wed Feb 12 13:22:00 2020)
  • running 3v solvent program (Wed Feb 12 13:22:00 2020)
  • imaging volume (download mrc) with UCSF Chimera (Wed Feb 12 13:22:00 2020)
  • UCSF Chimera created Jmol compatible file (Wed Feb 12 13:22:04 2020)
  • compressing 2020.feb12.122.obj (Wed Feb 12 13:22:04 2020)
  • UCSF Chimera completed in 4.12 sec (Wed Feb 12 13:22:04 2020)
  • analyzing volume (Wed Feb 12 13:22:04 2020)
  • normal CoM (1.7, -1.6, -3.8) Å (Wed Feb 12 13:22:06 2020)
  • reduced center failed (Wed Feb 12 13:22:06 2020)
  • volume analysis completed in 1.14 sec (Wed Feb 12 13:22:06 2020)
  • compressing 2020.feb12.122.mrc (Wed Feb 12 13:22:06 2020)
  • FINISHED (Wed Feb 12 13:22:06 2020)

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Log file display

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Terminal display
		
Message: converting pdb into xyzr 
/srv/output/2020/feb12/122 
Message: completed conversion of PDB file: 2020.feb12.122.pdb (size: 50k) 
Message: converted 1598 atoms of 1598 atoms 
Message: found 1598 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2020/feb12/122/2020.feb12.122.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2020.feb12.122.obj 
Message: UCSF Chimera completed in 4.12 sec 
OBJFILE /var/www/html/3vee/output/2020/feb12/122/2020.feb12.122.obj.gz 
Message: analyzing volume 
Message: normal CoM (1.7, -1.6, -3.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.14 sec 
Message: compressing 2020.feb12.122.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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