3v Running Log for JobId '2020.oct13.090'

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  • host ip address=67.80.165.210 (Tue Oct 13 10:44:49 2020)
  • converting pdb into xyzr (Tue Oct 13 10:44:49 2020)
  • completed conversion of PDB file: 2020.oct13.090.pdb (size: 552k) (Tue Oct 13 10:44:56 2020)
  • converted 17658 atoms of 17697 atoms (Tue Oct 13 10:44:56 2020)
  • found 17658 atoms in pdb (Tue Oct 13 10:44:56 2020)
  • running 3v solvent program (Tue Oct 13 10:44:56 2020)
  • imaging volume (download mrc) with UCSF Chimera (Tue Oct 13 10:45:40 2020)
  • UCSF Chimera created Jmol compatible file (Tue Oct 13 10:46:11 2020)
  • compressing 2020.oct13.090.obj (Tue Oct 13 10:46:11 2020)
  • UCSF Chimera completed in 42.39 sec (Tue Oct 13 10:46:22 2020)
  • analyzing volume (Tue Oct 13 10:46:22 2020)
  • normal CoM (-43.1, 15.8, 5.8) Å (Tue Oct 13 10:47:04 2020)
  • reduced center failed (Tue Oct 13 10:47:12 2020)
  • volume analysis completed in 49.42 sec (Tue Oct 13 10:47:12 2020)
  • compressing 2020.oct13.090.mrc (Tue Oct 13 10:47:12 2020)
  • FINISHED (Tue Oct 13 10:47:13 2020)

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Log file display

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Terminal display
		
Message: converting pdb into xyzr 
/srv/output/2020/oct13/090 
Message: completed conversion of PDB file: 2020.oct13.090.pdb (size: 552k) 
Message: converted 17658 atoms of 17697 atoms 
Message: found 17658 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2020/oct13/090/2020.oct13.090.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2020.oct13.090.obj 
Message: UCSF Chimera completed in 42.39 sec 
OBJFILE /var/www/html/3vee/output/2020/oct13/090/2020.oct13.090.obj.gz 
Message: analyzing volume 
Message: normal CoM (-43.1, 15.8, 5.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 49.42 sec 
Message: compressing 2020.oct13.090.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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