3v Running Log for JobId '2020.oct16.026'

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  • host ip address=45.184.250.234 (Fri Oct 16 17:24:23 2020)
  • converting pdb into xyzr (Fri Oct 16 17:24:23 2020)
  • completed conversion of PDB file: 2020.oct16.026.pdb (size: 61k) (Fri Oct 16 17:24:24 2020)
  • converted 1960 atoms of 1960 atoms (Fri Oct 16 17:24:24 2020)
  • found 1960 atoms in pdb (Fri Oct 16 17:24:24 2020)
  • running 3v volume program (Fri Oct 16 17:24:24 2020)
  • smoothing out volume (Fri Oct 16 17:24:24 2020)
  • imaging volume (download mrc) with UCSF Chimera (Fri Oct 16 17:24:24 2020)
  • UCSF Chimera created Jmol compatible file (Fri Oct 16 17:24:33 2020)
  • compressing 2020.oct16.026.obj (Fri Oct 16 17:24:33 2020)
  • UCSF Chimera completed in 9.37 sec (Fri Oct 16 17:24:34 2020)
  • analyzing volume (Fri Oct 16 17:24:34 2020)
  • normal CoM (-1.9, 0.5, -1.2) Å (Fri Oct 16 17:24:34 2020)
  • reduced center failed (Fri Oct 16 17:24:34 2020)
  • volume analysis completed in 0.71 sec (Fri Oct 16 17:24:34 2020)
  • compressing 2020.oct16.026.mrc (Fri Oct 16 17:24:34 2020)
  • FINISHED (Fri Oct 16 17:24:34 2020)

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Log file display

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Terminal display
		
/srv/output/2020/oct16/026 
Message: completed conversion of PDB file: 2020.oct16.026.pdb (size: 61k) 
Message: converted 1960 atoms of 1960 atoms 
Message: found 1960 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2020/oct16/026/2020.oct16.026.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 2020.oct16.026.obj 
Message: UCSF Chimera completed in 9.37 sec 
OBJFILE /var/www/html/3vee/output/2020/oct16/026/2020.oct16.026.obj.gz 
Message: analyzing volume 
Message: normal CoM (-1.9, 0.5, -1.2) Å 
Message: reduced center failed 
Message: volume analysis completed in 0.71 sec 
Message: compressing 2020.oct16.026.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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