3v Running Log for JobId '2019.dec02.97d'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=130.179.244.50 (Mon Dec 2 17:49:00 2019)
  • converting pdb into xyzr (Mon Dec 2 17:49:00 2019)
  • completed conversion of PDB file: 2019.dec02.97d.pdb (size: 237k) (Mon Dec 2 17:49:05 2019)
  • converted 7576 atoms of 7576 atoms (Mon Dec 2 17:49:05 2019)
  • found 7576 atoms in pdb (Mon Dec 2 17:49:05 2019)
  • starting probe size 1.000 (Mon Dec 2 17:49:05 2019)
  • running 3v volume program (Mon Dec 2 17:49:05 2019)
  • smoothing out volume (Mon Dec 2 17:49:06 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 17:49:06 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 17:49:18 2019)
  • compressing 2019.dec02.97d-1.0.obj (Mon Dec 2 17:49:18 2019)
  • UCSF Chimera completed in 12.98 sec (Mon Dec 2 17:49:19 2019)
  • analyzing volume (Mon Dec 2 17:49:19 2019)
  • normal CoM (-15.7, -1.5, 9.0) Å (Mon Dec 2 17:49:24 2019)
  • reduced center failed (Mon Dec 2 17:49:25 2019)
  • volume analysis completed in 6.17 sec (Mon Dec 2 17:49:25 2019)
  • compressing 2019.dec02.97d-1.0.mrc (Mon Dec 2 17:49:25 2019)
  • starting probe size 4.000 (Mon Dec 2 17:49:26 2019)
  • running 3v volume program (Mon Dec 2 17:49:26 2019)
  • smoothing out volume (Mon Dec 2 17:49:27 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 17:49:27 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 17:49:39 2019)
  • compressing 2019.dec02.97d-4.0.obj (Mon Dec 2 17:49:39 2019)
  • UCSF Chimera completed in 12.58 sec (Mon Dec 2 17:49:39 2019)
  • analyzing volume (Mon Dec 2 17:49:39 2019)
  • normal CoM (-15.7, -1.5, 9.0) Å (Mon Dec 2 17:49:46 2019)
  • reduced center failed (Mon Dec 2 17:49:47 2019)
  • volume analysis completed in 7.93 sec (Mon Dec 2 17:49:47 2019)
  • compressing 2019.dec02.97d-4.0.mrc (Mon Dec 2 17:49:47 2019)
  • starting probe size 7.000 (Mon Dec 2 17:49:48 2019)
  • running 3v volume program (Mon Dec 2 17:49:48 2019)
  • smoothing out volume (Mon Dec 2 17:49:50 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 17:49:50 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 17:50:02 2019)
  • compressing 2019.dec02.97d-7.0.obj (Mon Dec 2 17:50:02 2019)
  • UCSF Chimera completed in 12.76 sec (Mon Dec 2 17:50:03 2019)
  • analyzing volume (Mon Dec 2 17:50:03 2019)
  • normal CoM (-15.7, -1.5, 9.0) Å (Mon Dec 2 17:50:11 2019)
  • reduced center failed (Mon Dec 2 17:50:13 2019)
  • volume analysis completed in 9.76 sec (Mon Dec 2 17:50:13 2019)
  • compressing 2019.dec02.97d-7.0.mrc (Mon Dec 2 17:50:13 2019)
  • tarring file list (Mon Dec 2 17:50:13 2019)
  • compressing 2019.dec02.97d-1.0.mrc (Mon Dec 2 17:50:13 2019)
  • compressing 2019.dec02.97d-4.0.mrc (Mon Dec 2 17:50:13 2019)
  • compressing 2019.dec02.97d-7.0.mrc (Mon Dec 2 17:50:13 2019)
  • FINISHED (Mon Dec 2 17:50:13 2019)

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Log file display

Show last lines of log file 
Terminal display
		
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/dec02/97d/2019.dec02.97d-7.0.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.dec02.97d-7.0.obj 
Message: UCSF Chimera completed in 12.76 sec 
OBJFILE /var/www/html/3vee/output/2019/dec02/97d/2019.dec02.97d-7.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-15.7, -1.5, 9.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 9.76 sec 
Message: compressing 2019.dec02.97d-7.0.mrc 
Message: tarring file list 
Message: compressing 2019.dec02.97d-1.0.mrc 
Message: compressing 2019.dec02.97d-4.0.mrc 
Message: compressing 2019.dec02.97d-7.0.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
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If you find this useful or want more functionality please contact Neil <vossman77 [at] gmail [dot] com>
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