3v Running Log for JobId '2017.aug11.dfd'

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  • host ip address=79.74.193.39 (Fri Aug 11 14:35:54 2017)
  • converting pdb into xyzr (Fri Aug 11 14:35:54 2017)
  • completed conversion of PDB file: 2017.aug11.dfd.pdb (size: 47k) (Fri Aug 11 14:35:55 2017)
  • converted 1517 atoms of 1517 atoms (Fri Aug 11 14:35:55 2017)
  • found 1517 atoms in pdb (Fri Aug 11 14:35:55 2017)
  • running 3v volume program (Fri Aug 11 14:35:55 2017)
  • trimming mrc volume (Fri Aug 11 14:35:56 2017)
  • trimmed MRC file: /var/www/html/3vee/output/2017/aug11/dfd/2017.aug11.dfd-trim.mrc (Fri Aug 11 14:35:56 2017)
  • imaging volume (download mrc) with UCSF Chimera (Fri Aug 11 14:35:56 2017)
  • UCSF Chimera created 3D printing compatible file (Fri Aug 11 14:36:05 2017)
  • UCSF Chimera completed in 9.01 sec (Fri Aug 11 14:36:05 2017)
  • analyzing volume (Fri Aug 11 14:36:05 2017)
  • normal CoM (-8.5, -0.5, 2.4) Å (Fri Aug 11 14:36:13 2017)
  • reduced center failed (Fri Aug 11 14:36:15 2017)
  • volume analysis completed in 9.61 sec (Fri Aug 11 14:36:15 2017)
  • Created virtual frame buffer on port :8803 (Fri Aug 11 14:36:15 2017)
  • Please wait: Quadraitc decimating x3d volume and converting to STL using meshlab (Fri Aug 11 14:36:15 2017)
  • decimated STL file: /var/www/html/3vee/output/2017/aug11/dfd/2017.aug11.dfd-trim.stl (Fri Aug 11 14:36:17 2017)
  • MeshLab completed in 2.24 sec (Fri Aug 11 14:36:17 2017)
  • FINISHED (Fri Aug 11 14:36:17 2017)

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Log file display

Show last lines of log file 
Terminal display
		
Message: converted 1517 atoms of 1517 atoms 
Message: found 1517 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2017/aug11/dfd/2017.aug11.dfd.mrc 
Message: trimming mrc volume 
Message: trimmed MRC file: /var/www/html/3vee/output/2017/aug11/dfd/2017.aug11.dfd-trim.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created 3D printing compatible file 
Message: UCSF Chimera completed in 9.01 sec 
Message: analyzing volume 
Message: normal CoM (-8.5, -0.5, 2.4) Å 
Message: reduced center failed 
Message: volume analysis completed in 9.61 sec 
Message: Created virtual frame buffer on port :8803 
Message: Please wait: Quadraitc decimating x3d volume and converting to STL using meshlab 
Message: decimated STL file: /var/www/html/3vee/output/2017/aug11/dfd/2017.aug11.dfd-trim.stl 
Message: MeshLab completed in 2.24 sec 
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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