3v Running Log for JobId '2018.nov07.39a'

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  • host ip address=14.139.160.240 (Wed Nov 7 05:35:07 2018)
  • converting pdb into xyzr (Wed Nov 7 05:35:08 2018)
  • completed conversion of PDB file: 2018.nov07.39a.pdb (size: 51k) (Wed Nov 7 05:35:09 2018)
  • converted 1632 atoms of 1632 atoms (Wed Nov 7 05:35:09 2018)
  • found 1632 atoms in pdb (Wed Nov 7 05:35:09 2018)
  • running 3v volume program (Wed Nov 7 05:35:09 2018)
  • smoothing out volume (Wed Nov 7 05:35:09 2018)
  • imaging volume (download mrc) with UCSF Chimera (Wed Nov 7 05:35:09 2018)
  • UCSF Chimera created Jmol compatible file (Wed Nov 7 05:35:17 2018)
  • compressing 2018.nov07.39a.obj (Wed Nov 7 05:35:17 2018)
  • UCSF Chimera completed in 8.0 sec (Wed Nov 7 05:35:17 2018)
  • analyzing volume (Wed Nov 7 05:35:17 2018)
  • normal CoM (4.4, 2.0, -8.3) Å (Wed Nov 7 05:35:18 2018)
  • reduced center failed (Wed Nov 7 05:35:18 2018)
  • volume analysis completed in 1.04 sec (Wed Nov 7 05:35:18 2018)
  • compressing 2018.nov07.39a.mrc (Wed Nov 7 05:35:18 2018)
  • FINISHED (Wed Nov 7 05:35:18 2018)

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Log file display

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Terminal display
		
/srv/output/2018/nov07/39a 
Message: completed conversion of PDB file: 2018.nov07.39a.pdb (size: 51k) 
Message: converted 1632 atoms of 1632 atoms 
Message: found 1632 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2018/nov07/39a/2018.nov07.39a.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 2018.nov07.39a.obj 
Message: UCSF Chimera completed in 8.0 sec 
OBJFILE /var/www/html/3vee/output/2018/nov07/39a/2018.nov07.39a.obj.gz 
Message: analyzing volume 
Message: normal CoM (4.4, 2.0, -8.3) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.04 sec 
Message: compressing 2018.nov07.39a.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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