3v Running Log for JobId '2017.mar14.ef0'

Program is still running, progress is shown below

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  • host ip address=146.137.70.71 (Tue Mar 14 13:53:05 2017)
  • downloading pdb file (Tue Mar 14 13:53:05 2017)
  • completed download of PDB id 4mec (size: 301 k, 3808 lines) (Tue Mar 14 13:53:05 2017)
  • converting pdb into xyzr (Tue Mar 14 13:53:05 2017)
  • completed conversion of PDB file: 4mec-2017.mar14.ef0.pdb (size: 54k) (Tue Mar 14 13:53:07 2017)
  • converted 1734 atoms of 1734 atoms (Tue Mar 14 13:53:07 2017)
  • found 1734 atoms in pdb (Tue Mar 14 13:53:07 2017)
  • running 3v volume program (Tue Mar 14 13:53:07 2017)
  • smoothing out volume (Tue Mar 14 13:53:07 2017)
  • imaging volume (download mrc) with UCSF Chimera (Tue Mar 14 13:53:07 2017)
  • UCSF Chimera created Jmol compatible file (Tue Mar 14 13:53:15 2017)
  • compressing 4mec-2017.mar14.ef0.obj (Tue Mar 14 13:53:15 2017)
  • UCSF Chimera completed in 8.38 sec (Tue Mar 14 13:53:15 2017)
  • analyzing volume (Tue Mar 14 13:53:15 2017)
  • normal CoM (-1.7, -2.6, -3.9) Å (Tue Mar 14 13:53:16 2017)
  • reduced center failed (Tue Mar 14 13:53:16 2017)
  • volume analysis completed in 1.19 sec (Tue Mar 14 13:53:16 2017)
  • compressing 4mec-2017.mar14.ef0.mrc (Tue Mar 14 13:53:16 2017)
  • FINISHED (Tue Mar 14 13:53:16 2017)

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Log file display

Show last lines of log file 
Terminal display
		
/var/www/html/output/2017/mar14/ef0 
Message: completed conversion of PDB file: 4mec-2017.mar14.ef0.pdb (size: 54k) 
Message: converted 1734 atoms of 1734 atoms 
Message: found 1734 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2017/mar14/ef0/4mec-2017.mar14.ef0.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 4mec-2017.mar14.ef0.obj 
Message: UCSF Chimera completed in 8.38 sec 
OBJFILE /var/www/html/3vee/output/2017/mar14/ef0/4mec-2017.mar14.ef0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-1.7, -2.6, -3.9) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.19 sec 
Message: compressing 4mec-2017.mar14.ef0.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] yahoo.com>
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