3v Running Log for JobId '2021.apr07.f8d'

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  • host ip address=98.247.86.204 (Wed Apr 7 13:42:54 2021)
  • converting pdb into xyzr (Wed Apr 7 13:42:55 2021)
  • completed conversion of PDB file: 2021.apr07.f8d.pdb (size: 73k) (Wed Apr 7 13:42:55 2021)
  • converted 2326 atoms of 2326 atoms (Wed Apr 7 13:42:55 2021)
  • found 2326 atoms in pdb (Wed Apr 7 13:42:55 2021)
  • running 3v solvent program (Wed Apr 7 13:42:55 2021)
  • imaging volume (download mrc) with UCSF Chimera (Wed Apr 7 13:42:56 2021)
  • UCSF Chimera created Jmol compatible file (Wed Apr 7 13:42:59 2021)
  • compressing 2021.apr07.f8d.obj (Wed Apr 7 13:42:59 2021)
  • UCSF Chimera completed in 3.39 sec (Wed Apr 7 13:42:59 2021)
  • analyzing volume (Wed Apr 7 13:42:59 2021)
  • normal CoM (-10.0, -5.7, 11.6) Å (Wed Apr 7 13:42:59 2021)
  • volume analysis completed in 197.82 msec (Wed Apr 7 13:42:59 2021)
  • compressing 2021.apr07.f8d.mrc (Wed Apr 7 13:42:59 2021)
  • FINISHED (Wed Apr 7 13:42:59 2021)

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Log file display

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Terminal display
		
Message: host ip address=98.247.86.204 
Message: converting pdb into xyzr 
/srv/output/2021/apr07/f8d 
Message: completed conversion of PDB file: 2021.apr07.f8d.pdb (size: 73k) 
Message: converted 2326 atoms of 2326 atoms 
Message: found 2326 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2021/apr07/f8d/2021.apr07.f8d.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2021.apr07.f8d.obj 
Message: UCSF Chimera completed in 3.39 sec 
OBJFILE /var/www/html/3vee/output/2021/apr07/f8d/2021.apr07.f8d.obj.gz 
Message: analyzing volume 
Message: normal CoM (-10.0, -5.7, 11.6) Å 
Message: volume analysis completed in 197.82 msec 
Message: compressing 2021.apr07.f8d.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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