3v Running Log for JobId '2018.feb11.391'

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  • host ip address=73.12.29.169 (Sun Feb 11 13:31:48 2018)
  • downloading pdb file (Sun Feb 11 13:31:48 2018)
  • failed to download pdb id: 5c7h (Sun Feb 11 13:31:48 2018)
  • trying download pdb id again without bio unit (Sun Feb 11 13:31:50 2018)
  • completed download of PDB id 5c7h (size: 458 k, 5784 lines) (Sun Feb 11 13:31:50 2018)
  • converting pdb into xyzr (Sun Feb 11 13:31:50 2018)
  • completed conversion of PDB file: 5c7h-2018.feb11.391.pdb (size: 69k) (Sun Feb 11 13:31:52 2018)
  • converted 2221 atoms of 2221 atoms (Sun Feb 11 13:31:52 2018)
  • found 2221 atoms in pdb (Sun Feb 11 13:31:52 2018)
  • running 3v volume program (Sun Feb 11 13:31:52 2018)
  • smoothing out volume (Sun Feb 11 13:31:52 2018)
  • imaging volume (download mrc) with UCSF Chimera (Sun Feb 11 13:31:52 2018)
  • UCSF Chimera created Jmol compatible file (Sun Feb 11 13:32:01 2018)
  • compressing 5c7h-2018.feb11.391.obj (Sun Feb 11 13:32:01 2018)
  • UCSF Chimera completed in 8.9 sec (Sun Feb 11 13:32:01 2018)
  • analyzing volume (Sun Feb 11 13:32:01 2018)
  • normal CoM (-5.7, -1.6, -1.5) Å (Sun Feb 11 13:32:02 2018)
  • reduced center failed (Sun Feb 11 13:32:02 2018)
  • volume analysis completed in 1.31 sec (Sun Feb 11 13:32:02 2018)
  • compressing 5c7h-2018.feb11.391.mrc (Sun Feb 11 13:32:02 2018)
  • FINISHED (Sun Feb 11 13:32:02 2018)

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Log file display

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Terminal display
		
/var/www/html/output/2018/feb11/391 
Message: completed conversion of PDB file: 5c7h-2018.feb11.391.pdb (size: 69k) 
Message: converted 2221 atoms of 2221 atoms 
Message: found 2221 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2018/feb11/391/5c7h-2018.feb11.391.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 5c7h-2018.feb11.391.obj 
Message: UCSF Chimera completed in 8.9 sec 
OBJFILE /var/www/html/3vee/output/2018/feb11/391/5c7h-2018.feb11.391.obj.gz 
Message: analyzing volume 
Message: normal CoM (-5.7, -1.6, -1.5) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.31 sec 
Message: compressing 5c7h-2018.feb11.391.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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