3v Running Log for JobId '2018.nov02.da6'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=163.1.132.250 (Fri Nov 2 10:44:58 2018)
  • converting pdb into xyzr (Fri Nov 2 10:44:58 2018)
  • completed conversion of PDB file: 2018.nov02.da6.pdb (size: 250k) (Fri Nov 2 10:45:04 2018)
  • converted 8005 atoms of 8005 atoms (Fri Nov 2 10:45:04 2018)
  • found 8005 atoms in pdb (Fri Nov 2 10:45:04 2018)
  • running 3v volume program (Fri Nov 2 10:45:04 2018)
  • smoothing out volume (Fri Nov 2 10:45:06 2018)
  • imaging volume (download mrc) with UCSF Chimera (Fri Nov 2 10:45:07 2018)
  • UCSF Chimera created Jmol compatible file (Fri Nov 2 10:45:20 2018)
  • compressing 2018.nov02.da6.obj (Fri Nov 2 10:45:20 2018)
  • UCSF Chimera completed in 16.12 sec (Fri Nov 2 10:45:22 2018)
  • analyzing volume (Fri Nov 2 10:45:22 2018)
  • normal CoM (-3.6, 3.1, 2.9) Å (Fri Nov 2 10:46:00 2018)
  • reduced center failed (Fri Nov 2 10:46:10 2018)
  • volume analysis completed in 48.1 sec (Fri Nov 2 10:46:10 2018)
  • compressing 2018.nov02.da6.mrc (Fri Nov 2 10:46:10 2018)
  • FINISHED (Fri Nov 2 10:46:13 2018)

hit reload to refresh this page



Log file display

Show last lines of log file 
Terminal display
		
/srv/output/2018/nov02/da6 
Message: completed conversion of PDB file: 2018.nov02.da6.pdb (size: 250k) 
Message: converted 8005 atoms of 8005 atoms 
Message: found 8005 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2018/nov02/da6/2018.nov02.da6.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 2018.nov02.da6.obj 
Message: UCSF Chimera completed in 16.12 sec 
OBJFILE /var/www/html/3vee/output/2018/nov02/da6/2018.nov02.da6.obj.gz 
Message: analyzing volume 
Message: normal CoM (-3.6, 3.1, 2.9) Å 
Message: reduced center failed 
Message: volume analysis completed in 48.1 sec 
Message: compressing 2018.nov02.da6.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] gmail [dot] com>
back to main page