3v Running Log for JobId '2019.jun25.7c0'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=122.116.71.154 (Tue Jun 25 23:57:20 2019)
  • converting pdb into xyzr (Tue Jun 25 23:57:20 2019)
  • completed conversion of PDB file: 2019.jun25.7c0.pdb (size: 29k) (Tue Jun 25 23:57:21 2019)
  • converted 941 atoms of 941 atoms (Tue Jun 25 23:57:21 2019)
  • found 941 atoms in pdb (Tue Jun 25 23:57:21 2019)
  • starting probe size 0.000 (Tue Jun 25 23:57:21 2019)
  • running 3v volume program (Tue Jun 25 23:57:21 2019)
  • smoothing out volume (Tue Jun 25 23:57:21 2019)
  • imaging volume (download mrc) with UCSF Chimera (Tue Jun 25 23:57:21 2019)
  • UCSF Chimera created Jmol compatible file (Tue Jun 25 23:57:26 2019)
  • compressing 2019.jun25.7c0-0.0.obj (Tue Jun 25 23:57:26 2019)
  • UCSF Chimera completed in 4.87 sec (Tue Jun 25 23:57:26 2019)
  • analyzing volume (Tue Jun 25 23:57:26 2019)
  • normal CoM (-17.4, -0.5, 14.5) Å (Tue Jun 25 23:57:26 2019)
  • reduced center failed (Tue Jun 25 23:57:26 2019)
  • volume analysis completed in 321.45 msec (Tue Jun 25 23:57:26 2019)
  • compressing 2019.jun25.7c0-0.0.mrc (Tue Jun 25 23:57:26 2019)
  • starting probe size 3.000 (Tue Jun 25 23:57:26 2019)
  • running 3v volume program (Tue Jun 25 23:57:26 2019)
  • smoothing out volume (Tue Jun 25 23:57:26 2019)
  • imaging volume (download mrc) with UCSF Chimera (Tue Jun 25 23:57:26 2019)
  • UCSF Chimera created Jmol compatible file (Tue Jun 25 23:57:32 2019)
  • compressing 2019.jun25.7c0-3.0.obj (Tue Jun 25 23:57:32 2019)
  • UCSF Chimera completed in 5.95 sec (Tue Jun 25 23:57:32 2019)
  • analyzing volume (Tue Jun 25 23:57:32 2019)
  • normal CoM (-15.2, -0.5, 14.4) Å (Tue Jun 25 23:57:33 2019)
  • reduced center failed (Tue Jun 25 23:57:33 2019)
  • volume analysis completed in 0.5 sec (Tue Jun 25 23:57:33 2019)
  • compressing 2019.jun25.7c0-3.0.mrc (Tue Jun 25 23:57:33 2019)
  • starting probe size 6.000 (Tue Jun 25 23:57:33 2019)
  • running 3v volume program (Tue Jun 25 23:57:33 2019)
  • smoothing out volume (Tue Jun 25 23:57:33 2019)
  • imaging volume (download mrc) with UCSF Chimera (Tue Jun 25 23:57:33 2019)
  • UCSF Chimera created Jmol compatible file (Tue Jun 25 23:57:39 2019)
  • compressing 2019.jun25.7c0-6.0.obj (Tue Jun 25 23:57:39 2019)
  • UCSF Chimera completed in 5.41 sec (Tue Jun 25 23:57:39 2019)
  • analyzing volume (Tue Jun 25 23:57:39 2019)
  • normal CoM (-13.2, -0.6, 10.2) Å (Tue Jun 25 23:57:39 2019)
  • reduced center failed (Tue Jun 25 23:57:39 2019)
  • volume analysis completed in 0.59 sec (Tue Jun 25 23:57:39 2019)
  • compressing 2019.jun25.7c0-6.0.mrc (Tue Jun 25 23:57:39 2019)
  • starting probe size 9.000 (Tue Jun 25 23:57:39 2019)
  • running 3v volume program (Tue Jun 25 23:57:39 2019)
  • smoothing out volume (Tue Jun 25 23:57:41 2019)
  • imaging volume (download mrc) with UCSF Chimera (Tue Jun 25 23:57:41 2019)
  • UCSF Chimera created Jmol compatible file (Tue Jun 25 23:57:46 2019)
  • compressing 2019.jun25.7c0-9.0.obj (Tue Jun 25 23:57:46 2019)
  • UCSF Chimera completed in 5.72 sec (Tue Jun 25 23:57:46 2019)
  • analyzing volume (Tue Jun 25 23:57:46 2019)
  • normal CoM (-13.1, -0.6, 10.2) Å (Tue Jun 25 23:57:47 2019)
  • reduced center failed (Tue Jun 25 23:57:47 2019)
  • volume analysis completed in 1.01 sec (Tue Jun 25 23:57:47 2019)
  • compressing 2019.jun25.7c0-9.0.mrc (Tue Jun 25 23:57:47 2019)
  • tarring file list (Tue Jun 25 23:57:47 2019)
  • compressing 2019.jun25.7c0-0.0.mrc (Tue Jun 25 23:57:47 2019)
  • compressing 2019.jun25.7c0-3.0.mrc (Tue Jun 25 23:57:47 2019)
  • compressing 2019.jun25.7c0-6.0.mrc (Tue Jun 25 23:57:47 2019)
  • compressing 2019.jun25.7c0-9.0.mrc (Tue Jun 25 23:57:47 2019)
  • FINISHED (Tue Jun 25 23:57:47 2019)

hit reload to refresh this page



Log file display

Show last lines of log file 
Terminal display
		
wrote to mrc file: /var/www/html/3vee/output/2019/jun25/7c0/2019.jun25.7c0-9.0.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 2019.jun25.7c0-9.0.obj 
Message: UCSF Chimera completed in 5.72 sec 
OBJFILE /var/www/html/3vee/output/2019/jun25/7c0/2019.jun25.7c0-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-13.1, -0.6, 10.2) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.01 sec 
Message: compressing 2019.jun25.7c0-9.0.mrc 
Message: tarring file list 
Message: compressing 2019.jun25.7c0-0.0.mrc 
Message: compressing 2019.jun25.7c0-3.0.mrc 
Message: compressing 2019.jun25.7c0-6.0.mrc 
Message: compressing 2019.jun25.7c0-9.0.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