3v Running Log for JobId '2017.mar15.805'

Program is still running, progress is shown below

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  • host ip address=190.242.62.242 (Wed Mar 15 12:25:19 2017)
  • downloading pdb file (Wed Mar 15 12:25:19 2017)
  • completed download of PDB id 2vnm (size: 282 k, 3571 lines) (Wed Mar 15 12:25:20 2017)
  • converting pdb into xyzr (Wed Mar 15 12:25:20 2017)
  • completed conversion of PDB file: 2vnm-2017.mar15.805.pdb (size: 93k) (Wed Mar 15 12:25:22 2017)
  • converted 2991 atoms of 2991 atoms (Wed Mar 15 12:25:22 2017)
  • found 2991 atoms in pdb (Wed Mar 15 12:25:22 2017)
  • running 3v volume program (Wed Mar 15 12:25:22 2017)
  • smoothing out volume (Wed Mar 15 12:25:22 2017)
  • imaging volume (download mrc) with UCSF Chimera (Wed Mar 15 12:25:22 2017)
  • UCSF Chimera created Jmol compatible file (Wed Mar 15 12:25:30 2017)
  • compressing 2vnm-2017.mar15.805.obj (Wed Mar 15 12:25:30 2017)
  • UCSF Chimera completed in 7.84 sec (Wed Mar 15 12:25:30 2017)
  • analyzing volume (Wed Mar 15 12:25:30 2017)
  • normal CoM (13.3, 1.2, -14.1) Å (Wed Mar 15 12:25:31 2017)
  • reduced center failed (Wed Mar 15 12:25:32 2017)
  • volume analysis completed in 1.75 sec (Wed Mar 15 12:25:32 2017)
  • compressing 2vnm-2017.mar15.805.mrc (Wed Mar 15 12:25:32 2017)
  • FINISHED (Wed Mar 15 12:25:32 2017)

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Log file display

Show last lines of log file 
Terminal display
		
/var/www/html/output/2017/mar15/805 
Message: completed conversion of PDB file: 2vnm-2017.mar15.805.pdb (size: 93k) 
Message: converted 2991 atoms of 2991 atoms 
Message: found 2991 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2017/mar15/805/2vnm-2017.mar15.805.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 2vnm-2017.mar15.805.obj 
Message: UCSF Chimera completed in 7.84 sec 
OBJFILE /var/www/html/3vee/output/2017/mar15/805/2vnm-2017.mar15.805.obj.gz 
Message: analyzing volume 
Message: normal CoM (13.3, 1.2, -14.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.75 sec 
Message: compressing 2vnm-2017.mar15.805.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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