3v Running Log for JobId '2017.apr20.89a'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=108.176.246.85 (Thu Apr 20 22:34:14 2017)
  • converting pdb into xyzr (Thu Apr 20 22:34:14 2017)
  • completed conversion of PDB file: 2017.apr20.89a.pdb (size: 208k) (Thu Apr 20 22:34:16 2017)
  • converted 6667 atoms of 6667 atoms (Thu Apr 20 22:34:16 2017)
  • found 6667 atoms in pdb (Thu Apr 20 22:34:16 2017)
  • running 3v volume program (Thu Apr 20 22:34:16 2017)
  • smoothing out volume (Thu Apr 20 22:34:17 2017)
  • imaging volume (download mrc) with UCSF Chimera (Thu Apr 20 22:34:17 2017)
  • UCSF Chimera created Jmol compatible file (Thu Apr 20 22:34:29 2017)
  • compressing 2017.apr20.89a.obj (Thu Apr 20 22:34:29 2017)
  • UCSF Chimera completed in 13.28 sec (Thu Apr 20 22:34:30 2017)
  • analyzing volume (Thu Apr 20 22:34:30 2017)
  • normal CoM (12.8, 0.8, -13.0) Å (Thu Apr 20 22:34:37 2017)
  • reduced center failed (Thu Apr 20 22:34:39 2017)
  • volume analysis completed in 8.9 sec (Thu Apr 20 22:34:39 2017)
  • compressing 2017.apr20.89a.mrc (Thu Apr 20 22:34:39 2017)
  • FINISHED (Thu Apr 20 22:34:39 2017)

hit reload to refresh this page



Log file display

Show last lines of log file 
Terminal display
		
/var/www/html/output/2017/apr20/89a 
Message: completed conversion of PDB file: 2017.apr20.89a.pdb (size: 208k) 
Message: converted 6667 atoms of 6667 atoms 
Message: found 6667 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2017/apr20/89a/2017.apr20.89a.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.apr20.89a.obj 
Message: UCSF Chimera completed in 13.28 sec 
OBJFILE /var/www/html/3vee/output/2017/apr20/89a/2017.apr20.89a.obj.gz 
Message: analyzing volume 
Message: normal CoM (12.8, 0.8, -13.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 8.9 sec 
Message: compressing 2017.apr20.89a.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
Download source code
Help
Site news and updates
If you find this useful or want more functionality please contact Neil <vossman77 [at] yahoo.com>
back to main page