3v Running Log for JobId '2020.oct16.aa0'

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  • host ip address=45.184.250.234 (Fri Oct 16 17:30:11 2020)
  • converting pdb into xyzr (Fri Oct 16 17:30:11 2020)
  • completed conversion of PDB file: 2020.oct16.aa0.pdb (size: 61k) (Fri Oct 16 17:30:11 2020)
  • converted 1960 atoms of 1960 atoms (Fri Oct 16 17:30:11 2020)
  • found 1960 atoms in pdb (Fri Oct 16 17:30:11 2020)
  • running 3v volume program (Fri Oct 16 17:30:11 2020)
  • smoothing out volume (Fri Oct 16 17:30:12 2020)
  • imaging volume (download mrc) with UCSF Chimera (Fri Oct 16 17:30:12 2020)
  • UCSF Chimera created Jmol compatible file (Fri Oct 16 17:30:20 2020)
  • compressing 2020.oct16.aa0.obj (Fri Oct 16 17:30:20 2020)
  • UCSF Chimera completed in 8.21 sec (Fri Oct 16 17:30:20 2020)
  • analyzing volume (Fri Oct 16 17:30:20 2020)
  • normal CoM (0.0, 0.6, -5.1) Å (Fri Oct 16 17:30:20 2020)
  • reduced center failed (Fri Oct 16 17:30:20 2020)
  • volume analysis completed in 0.67 sec (Fri Oct 16 17:30:20 2020)
  • compressing 2020.oct16.aa0.mrc (Fri Oct 16 17:30:20 2020)
  • FINISHED (Fri Oct 16 17:30:21 2020)

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Log file display

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Terminal display
		
/srv/output/2020/oct16/aa0 
Message: completed conversion of PDB file: 2020.oct16.aa0.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/aa0/2020.oct16.aa0.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.aa0.obj 
Message: UCSF Chimera completed in 8.21 sec 
OBJFILE /var/www/html/3vee/output/2020/oct16/aa0/2020.oct16.aa0.obj.gz 
Message: analyzing volume 
Message: normal CoM (0.0, 0.6, -5.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 0.67 sec 
Message: compressing 2020.oct16.aa0.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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