3v Running Log for JobId '2023.may25.216'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=130.237.251.130 (Thu May 25 03:19:44 2023)
  • converting pdb into xyzr (Thu May 25 03:19:44 2023)
  • completed conversion of PDB file: 2023.may25.216.pdb (size: 99k) (Thu May 25 03:19:46 2023)
  • converted 3168 atoms of 3168 atoms (Thu May 25 03:19:46 2023)
  • found 3168 atoms in pdb (Thu May 25 03:19:46 2023)
  • running 3v volume program (Thu May 25 03:19:46 2023)
  • smoothing out volume (Thu May 25 03:19:47 2023)
  • imaging volume (download mrc) with UCSF Chimera (Thu May 25 03:19:47 2023)
  • UCSF Chimera created Jmol compatible file (Thu May 25 03:19:56 2023)
  • compressing 2023.may25.216.obj (Thu May 25 03:19:56 2023)
  • UCSF Chimera completed in 9.59 sec (Thu May 25 03:19:56 2023)
  • analyzing volume (Thu May 25 03:19:56 2023)
  • normal CoM (-7.8, -0.1, 1.1) Å (Thu May 25 03:19:58 2023)
  • reduced center failed (Thu May 25 03:19:58 2023)
  • volume analysis completed in 2.08 sec (Thu May 25 03:19:58 2023)
  • compressing 2023.may25.216.mrc (Thu May 25 03:19:58 2023)
  • FINISHED (Thu May 25 03:19:59 2023)

hit reload to refresh this page


Log file display

Show last lines of log file  
Terminal display
		
/srv/output/2023/may25/216 
Message: completed conversion of PDB file: 2023.may25.216.pdb (size: 99k) 
Message: converted 3168 atoms of 3168 atoms 
Message: found 3168 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2023/may25/216/2023.may25.216.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 2023.may25.216.obj 
Message: UCSF Chimera completed in 9.59 sec 
OBJFILE /var/www/html/3vee/output/2023/may25/216/2023.may25.216.obj.gz 
Message: analyzing volume 
Message: normal CoM (-7.8, -0.1, 1.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 2.08 sec 
Message: compressing 2023.may25.216.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