3v Running Log for JobId '2018.jan07.d22'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=37.170.63.99 (Sun Jan 7 10:24:49 2018)
  • converting pdb into xyzr (Sun Jan 7 10:24:50 2018)
  • completed conversion of PDB file: 2018.jan07.d22.pdb (size: 119k) (Sun Jan 7 10:24:51 2018)
  • converted 3793 atoms of 3793 atoms (Sun Jan 7 10:24:51 2018)
  • found 3793 atoms in pdb (Sun Jan 7 10:24:51 2018)
  • starting probe size 0.000 (Sun Jan 7 10:24:51 2018)
  • running 3v volume program (Sun Jan 7 10:24:51 2018)
  • smoothing out volume (Sun Jan 7 10:24:51 2018)
  • imaging volume (download mrc) with UCSF Chimera (Sun Jan 7 10:24:51 2018)
  • UCSF Chimera created Jmol compatible file (Sun Jan 7 10:24:58 2018)
  • compressing 2018.jan07.d22-0.0.obj (Sun Jan 7 10:24:58 2018)
  • UCSF Chimera completed in 7.41 sec (Sun Jan 7 10:24:58 2018)
  • analyzing volume (Sun Jan 7 10:24:58 2018)
  • normal CoM (0.7, 0.1, 1.9) Å (Sun Jan 7 10:24:59 2018)
  • reduced center failed (Sun Jan 7 10:24:59 2018)
  • volume analysis completed in 1.0 sec (Sun Jan 7 10:24:59 2018)
  • compressing 2018.jan07.d22-0.0.mrc (Sun Jan 7 10:24:59 2018)
  • starting probe size 3.000 (Sun Jan 7 10:25:00 2018)
  • running 3v volume program (Sun Jan 7 10:25:00 2018)
  • smoothing out volume (Sun Jan 7 10:25:00 2018)
  • imaging volume (download mrc) with UCSF Chimera (Sun Jan 7 10:25:00 2018)
  • UCSF Chimera created Jmol compatible file (Sun Jan 7 10:25:08 2018)
  • compressing 2018.jan07.d22-3.0.obj (Sun Jan 7 10:25:08 2018)
  • UCSF Chimera completed in 8.35 sec (Sun Jan 7 10:25:08 2018)
  • analyzing volume (Sun Jan 7 10:25:08 2018)
  • normal CoM (2.5, -0.3, -0.1) Å (Sun Jan 7 10:25:09 2018)
  • reduced center failed (Sun Jan 7 10:25:10 2018)
  • volume analysis completed in 1.46 sec (Sun Jan 7 10:25:10 2018)
  • compressing 2018.jan07.d22-3.0.mrc (Sun Jan 7 10:25:10 2018)
  • starting probe size 6.000 (Sun Jan 7 10:25:10 2018)
  • running 3v volume program (Sun Jan 7 10:25:10 2018)
  • smoothing out volume (Sun Jan 7 10:25:10 2018)
  • imaging volume (download mrc) with UCSF Chimera (Sun Jan 7 10:25:10 2018)
  • UCSF Chimera created Jmol compatible file (Sun Jan 7 10:25:18 2018)
  • compressing 2018.jan07.d22-6.0.obj (Sun Jan 7 10:25:18 2018)
  • UCSF Chimera completed in 8.09 sec (Sun Jan 7 10:25:18 2018)
  • analyzing volume (Sun Jan 7 10:25:18 2018)
  • normal CoM (-1.6, -0.5, 1.8) Å (Sun Jan 7 10:25:20 2018)
  • reduced center failed (Sun Jan 7 10:25:20 2018)
  • volume analysis completed in 1.85 sec (Sun Jan 7 10:25:20 2018)
  • compressing 2018.jan07.d22-6.0.mrc (Sun Jan 7 10:25:20 2018)
  • starting probe size 9.000 (Sun Jan 7 10:25:20 2018)
  • running 3v volume program (Sun Jan 7 10:25:20 2018)
  • smoothing out volume (Sun Jan 7 10:25:21 2018)
  • imaging volume (download mrc) with UCSF Chimera (Sun Jan 7 10:25:21 2018)
  • UCSF Chimera created Jmol compatible file (Sun Jan 7 10:25:28 2018)
  • compressing 2018.jan07.d22-9.0.obj (Sun Jan 7 10:25:28 2018)
  • UCSF Chimera completed in 7.73 sec (Sun Jan 7 10:25:29 2018)
  • analyzing volume (Sun Jan 7 10:25:29 2018)
  • normal CoM (-1.9, -2.7, 1.8) Å (Sun Jan 7 10:25:30 2018)
  • reduced center failed (Sun Jan 7 10:25:31 2018)
  • volume analysis completed in 2.31 sec (Sun Jan 7 10:25:31 2018)
  • compressing 2018.jan07.d22-9.0.mrc (Sun Jan 7 10:25:31 2018)
  • tarring file list (Sun Jan 7 10:25:31 2018)
  • compressing 2018.jan07.d22-0.0.mrc (Sun Jan 7 10:25:31 2018)
  • compressing 2018.jan07.d22-3.0.mrc (Sun Jan 7 10:25:31 2018)
  • compressing 2018.jan07.d22-6.0.mrc (Sun Jan 7 10:25:31 2018)
  • compressing 2018.jan07.d22-9.0.mrc (Sun Jan 7 10:25:31 2018)
  • FINISHED (Sun Jan 7 10:25:31 2018)

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Log file display

Show last lines of log file 
Terminal display
		
wrote to mrc file: /var/www/html/3vee/output/2018/jan07/d22/2018.jan07.d22-9.0.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 2018.jan07.d22-9.0.obj 
Message: UCSF Chimera completed in 7.73 sec 
OBJFILE /var/www/html/3vee/output/2018/jan07/d22/2018.jan07.d22-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-1.9, -2.7, 1.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 2.31 sec 
Message: compressing 2018.jan07.d22-9.0.mrc 
Message: tarring file list 
Message: compressing 2018.jan07.d22-0.0.mrc 
Message: compressing 2018.jan07.d22-3.0.mrc 
Message: compressing 2018.jan07.d22-6.0.mrc 
Message: compressing 2018.jan07.d22-9.0.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
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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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