3v Running Log for JobId '2020.oct01.f79'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=140.254.255.254 (Thu Oct 1 16:43:34 2020)
  • converting pdb into xyzr (Thu Oct 1 16:43:34 2020)
  • completed conversion of PDB file: 2020.oct01.f79.pdb (size: 4k) (Thu Oct 1 16:43:34 2020)
  • converted 139 atoms of 139 atoms (Thu Oct 1 16:43:34 2020)
  • found 139 atoms in pdb (Thu Oct 1 16:43:34 2020)
  • running 3v channel program (Thu Oct 1 16:43:34 2020)
  • smoothing out volume (Thu Oct 1 16:43:37 2020)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 1 16:43:37 2020)
  • UCSF Chimera created Jmol compatible file (Thu Oct 1 16:43:45 2020)
  • compressing 2020.oct01.f79.obj (Thu Oct 1 16:43:45 2020)
  • UCSF Chimera completed in 7.77 sec (Thu Oct 1 16:43:45 2020)
  • analyzing volume (Thu Oct 1 16:43:45 2020)
  • normal CoM (-18.3, -16.0, -13.9) Å (Thu Oct 1 16:43:45 2020)
  • reduced center failed (Thu Oct 1 16:43:45 2020)
  • volume analysis completed in 54.5 msec (Thu Oct 1 16:43:45 2020)
  • compressing 2020.oct01.f79.mrc (Thu Oct 1 16:43:45 2020)
  • FINISHED (Thu Oct 1 16:43:45 2020)

hit reload to refresh this page



Log file display

Show last lines of log file 
Terminal display
		
Message: converting pdb into xyzr 
/srv/output/2020/oct01/f79 
Message: completed conversion of PDB file: 2020.oct01.f79.pdb (size: 4k) 
Message: converted 139 atoms of 139 atoms 
Message: found 139 atoms in pdb 
Message: running 3v channel program 
wrote to file: /var/www/html/3vee/output/2020/oct01/f79/2020.oct01.f79.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 2020.oct01.f79.obj 
Message: UCSF Chimera completed in 7.77 sec 
Message: analyzing volume 
Message: normal CoM (-18.3, -16.0, -13.9) Å 
Message: reduced center failed 
Message: volume analysis completed in 54.5 msec 
Message: compressing 2020.oct01.f79.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