3v Running Log for JobId '2017.mar17.ea3'

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  • host ip address=103.21.125.76 (Fri Mar 17 03:07:24 2017)
  • converting pdb into xyzr (Fri Mar 17 03:07:24 2017)
  • completed conversion of PDB file: 2017.mar17.ea3.pdb (size: 1k) (Fri Mar 17 03:07:24 2017)
  • converted 47 atoms of 47 atoms (Fri Mar 17 03:07:24 2017)
  • found 47 atoms in pdb (Fri Mar 17 03:07:24 2017)
  • running 3v volume program (Fri Mar 17 03:07:24 2017)
  • smoothing out volume (Fri Mar 17 03:07:24 2017)
  • imaging volume (download mrc) with UCSF Chimera (Fri Mar 17 03:07:24 2017)
  • UCSF Chimera created Jmol compatible file (Fri Mar 17 03:07:27 2017)
  • compressing 2017.mar17.ea3.obj (Fri Mar 17 03:07:27 2017)
  • UCSF Chimera completed in 3.11 sec (Fri Mar 17 03:07:27 2017)
  • analyzing volume (Fri Mar 17 03:07:27 2017)
  • normal CoM (-2.3, -1.5, 0.3) Å (Fri Mar 17 03:07:28 2017)
  • reduced center failed (Fri Mar 17 03:07:28 2017)
  • volume analysis completed in 336.01 msec (Fri Mar 17 03:07:28 2017)
  • compressing 2017.mar17.ea3.mrc (Fri Mar 17 03:07:28 2017)
  • FINISHED (Fri Mar 17 03:07:28 2017)

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Log file display

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Terminal display
		
/var/www/html/output/2017/mar17/ea3 
Message: completed conversion of PDB file: 2017.mar17.ea3.pdb (size: 1k) 
Message: converted 47 atoms of 47 atoms 
Message: found 47 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2017/mar17/ea3/2017.mar17.ea3.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 2017.mar17.ea3.obj 
Message: UCSF Chimera completed in 3.11 sec 
OBJFILE /var/www/html/3vee/output/2017/mar17/ea3/2017.mar17.ea3.obj.gz 
Message: analyzing volume 
Message: normal CoM (-2.3, -1.5, 0.3) Å 
Message: reduced center failed 
Message: volume analysis completed in 336.01 msec 
Message: compressing 2017.mar17.ea3.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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