3v Running Log for JobId '2020.oct12.638'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=73.145.137.39 (Mon Oct 12 18:17:38 2020)
  • converting pdb into xyzr (Mon Oct 12 18:17:38 2020)
  • completed conversion of PDB file: 2020.oct12.638.pdb (size: 0k) (Mon Oct 12 18:17:38 2020)
  • converted 10 atoms of 10 atoms (Mon Oct 12 18:17:38 2020)
  • found 10 atoms in pdb (Mon Oct 12 18:17:38 2020)
  • starting probe size 0.000 (Mon Oct 12 18:17:38 2020)
  • running 3v volume program (Mon Oct 12 18:17:38 2020)
  • smoothing out volume (Mon Oct 12 18:17:38 2020)
  • imaging volume (download mrc) with UCSF Chimera (Mon Oct 12 18:17:38 2020)
  • UCSF Chimera created Jmol compatible file (Mon Oct 12 18:17:40 2020)
  • compressing 2020.oct12.638-0.0.obj (Mon Oct 12 18:17:40 2020)
  • UCSF Chimera completed in 1.95 sec (Mon Oct 12 18:17:40 2020)
  • analyzing volume (Mon Oct 12 18:17:40 2020)
  • normal CoM (-4.0, 0.7, 2.9) Å (Mon Oct 12 18:17:40 2020)
  • reduced center failed (Mon Oct 12 18:17:40 2020)
  • volume analysis completed in 36.46 msec (Mon Oct 12 18:17:40 2020)
  • compressing 2020.oct12.638-0.0.mrc (Mon Oct 12 18:17:40 2020)
  • starting probe size 3.000 (Mon Oct 12 18:17:40 2020)
  • running 3v volume program (Mon Oct 12 18:17:40 2020)
  • smoothing out volume (Mon Oct 12 18:17:40 2020)
  • imaging volume (download mrc) with UCSF Chimera (Mon Oct 12 18:17:40 2020)
  • UCSF Chimera created Jmol compatible file (Mon Oct 12 18:17:47 2020)
  • compressing 2020.oct12.638-3.0.obj (Mon Oct 12 18:17:47 2020)
  • UCSF Chimera completed in 6.42 sec (Mon Oct 12 18:17:47 2020)
  • analyzing volume (Mon Oct 12 18:17:47 2020)
  • normal CoM (-2.1, 0.8, 0.9) Å (Mon Oct 12 18:17:47 2020)
  • reduced center failed (Mon Oct 12 18:17:47 2020)
  • volume analysis completed in 61.95 msec (Mon Oct 12 18:17:47 2020)
  • compressing 2020.oct12.638-3.0.mrc (Mon Oct 12 18:17:47 2020)
  • starting probe size 6.000 (Mon Oct 12 18:17:47 2020)
  • running 3v volume program (Mon Oct 12 18:17:47 2020)
  • smoothing out volume (Mon Oct 12 18:17:47 2020)
  • imaging volume (download mrc) with UCSF Chimera (Mon Oct 12 18:17:47 2020)
  • UCSF Chimera created Jmol compatible file (Mon Oct 12 18:17:49 2020)
  • compressing 2020.oct12.638-6.0.obj (Mon Oct 12 18:17:49 2020)
  • UCSF Chimera completed in 1.95 sec (Mon Oct 12 18:17:49 2020)
  • analyzing volume (Mon Oct 12 18:17:49 2020)
  • normal CoM (-6.0, -1.3, 2.9) Å (Mon Oct 12 18:17:49 2020)
  • reduced center failed (Mon Oct 12 18:17:49 2020)
  • volume analysis completed in 104.77 msec (Mon Oct 12 18:17:49 2020)
  • compressing 2020.oct12.638-6.0.mrc (Mon Oct 12 18:17:49 2020)
  • starting probe size 9.000 (Mon Oct 12 18:17:49 2020)
  • running 3v volume program (Mon Oct 12 18:17:49 2020)
  • smoothing out volume (Mon Oct 12 18:17:49 2020)
  • imaging volume (download mrc) with UCSF Chimera (Mon Oct 12 18:17:49 2020)
  • UCSF Chimera created Jmol compatible file (Mon Oct 12 18:17:54 2020)
  • compressing 2020.oct12.638-9.0.obj (Mon Oct 12 18:17:54 2020)
  • UCSF Chimera completed in 5.08 sec (Mon Oct 12 18:17:54 2020)
  • analyzing volume (Mon Oct 12 18:17:54 2020)
  • normal CoM (-4.0, 0.8, 3.0) Å (Mon Oct 12 18:17:54 2020)
  • reduced center failed (Mon Oct 12 18:17:54 2020)
  • volume analysis completed in 165.72 msec (Mon Oct 12 18:17:54 2020)
  • compressing 2020.oct12.638-9.0.mrc (Mon Oct 12 18:17:54 2020)
  • tarring file list (Mon Oct 12 18:17:55 2020)
  • compressing 2020.oct12.638-0.0.mrc (Mon Oct 12 18:17:55 2020)
  • compressing 2020.oct12.638-3.0.mrc (Mon Oct 12 18:17:55 2020)
  • compressing 2020.oct12.638-6.0.mrc (Mon Oct 12 18:17:55 2020)
  • compressing 2020.oct12.638-9.0.mrc (Mon Oct 12 18:17:55 2020)
  • FINISHED (Mon Oct 12 18:17:55 2020)

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Log file display

Show last lines of log file 
Terminal display
		
wrote to mrc file: /var/www/html/3vee/output/2020/oct12/638/2020.oct12.638-9.0.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 2020.oct12.638-9.0.obj 
Message: UCSF Chimera completed in 5.08 sec 
OBJFILE /var/www/html/3vee/output/2020/oct12/638/2020.oct12.638-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-4.0, 0.8, 3.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 165.72 msec 
Message: compressing 2020.oct12.638-9.0.mrc 
Message: tarring file list 
Message: compressing 2020.oct12.638-0.0.mrc 
Message: compressing 2020.oct12.638-3.0.mrc 
Message: compressing 2020.oct12.638-6.0.mrc 
Message: compressing 2020.oct12.638-9.0.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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