3v Running Log for JobId '2020.jan08.03e'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=124.16.180.112 (Wed Jan 8 22:32:58 2020)
  • converting pdb into xyzr (Wed Jan 8 22:32:58 2020)
  • completed conversion of PDB file: 2020.jan08.03e.pdb (size: 31k) (Wed Jan 8 22:33:00 2020)
  • converted 999 atoms of 999 atoms (Wed Jan 8 22:33:00 2020)
  • found 999 atoms in pdb (Wed Jan 8 22:33:00 2020)
  • starting probe size 1.000 (Wed Jan 8 22:33:00 2020)
  • running 3v volume program (Wed Jan 8 22:33:00 2020)
  • smoothing out volume (Wed Jan 8 22:33:00 2020)
  • imaging volume (download mrc) with UCSF Chimera (Wed Jan 8 22:33:00 2020)
  • UCSF Chimera created Jmol compatible file (Wed Jan 8 22:33:06 2020)
  • compressing 2020.jan08.03e-1.0.obj (Wed Jan 8 22:33:06 2020)
  • UCSF Chimera completed in 5.43 sec (Wed Jan 8 22:33:06 2020)
  • analyzing volume (Wed Jan 8 22:33:06 2020)
  • normal CoM (-14.0, -0.8, 10.8) Å (Wed Jan 8 22:33:06 2020)
  • reduced center failed (Wed Jan 8 22:33:06 2020)
  • volume analysis completed in 321.7 msec (Wed Jan 8 22:33:06 2020)
  • compressing 2020.jan08.03e-1.0.mrc (Wed Jan 8 22:33:06 2020)
  • starting probe size 4.000 (Wed Jan 8 22:33:06 2020)
  • running 3v volume program (Wed Jan 8 22:33:06 2020)
  • smoothing out volume (Wed Jan 8 22:33:06 2020)
  • imaging volume (download mrc) with UCSF Chimera (Wed Jan 8 22:33:06 2020)
  • UCSF Chimera created Jmol compatible file (Wed Jan 8 22:33:12 2020)
  • compressing 2020.jan08.03e-4.0.obj (Wed Jan 8 22:33:12 2020)
  • UCSF Chimera completed in 5.64 sec (Wed Jan 8 22:33:12 2020)
  • analyzing volume (Wed Jan 8 22:33:12 2020)
  • normal CoM (-14.2, -0.7, 13.3) Å (Wed Jan 8 22:33:12 2020)
  • reduced center failed (Wed Jan 8 22:33:12 2020)
  • volume analysis completed in 482.31 msec (Wed Jan 8 22:33:12 2020)
  • compressing 2020.jan08.03e-4.0.mrc (Wed Jan 8 22:33:12 2020)
  • starting probe size 7.000 (Wed Jan 8 22:33:12 2020)
  • running 3v volume program (Wed Jan 8 22:33:12 2020)
  • smoothing out volume (Wed Jan 8 22:33:12 2020)
  • imaging volume (download mrc) with UCSF Chimera (Wed Jan 8 22:33:12 2020)
  • UCSF Chimera created Jmol compatible file (Wed Jan 8 22:33:19 2020)
  • compressing 2020.jan08.03e-7.0.obj (Wed Jan 8 22:33:19 2020)
  • UCSF Chimera completed in 6.24 sec (Wed Jan 8 22:33:19 2020)
  • analyzing volume (Wed Jan 8 22:33:19 2020)
  • normal CoM (-14.3, -0.7, 13.1) Å (Wed Jan 8 22:33:19 2020)
  • reduced center failed (Wed Jan 8 22:33:19 2020)
  • volume analysis completed in 0.65 sec (Wed Jan 8 22:33:19 2020)
  • compressing 2020.jan08.03e-7.0.mrc (Wed Jan 8 22:33:19 2020)
  • starting probe size 10.000 (Wed Jan 8 22:33:19 2020)
  • running 3v volume program (Wed Jan 8 22:33:19 2020)
  • smoothing out volume (Wed Jan 8 22:33:20 2020)
  • imaging volume (download mrc) with UCSF Chimera (Wed Jan 8 22:33:20 2020)
  • UCSF Chimera created Jmol compatible file (Wed Jan 8 22:33:25 2020)
  • compressing 2020.jan08.03e-10.0.obj (Wed Jan 8 22:33:25 2020)
  • UCSF Chimera completed in 5.62 sec (Wed Jan 8 22:33:25 2020)
  • analyzing volume (Wed Jan 8 22:33:25 2020)
  • normal CoM (-16.5, -0.6, 11.1) Å (Wed Jan 8 22:33:26 2020)
  • reduced center failed (Wed Jan 8 22:33:26 2020)
  • volume analysis completed in 0.84 sec (Wed Jan 8 22:33:26 2020)
  • compressing 2020.jan08.03e-10.0.mrc (Wed Jan 8 22:33:26 2020)
  • tarring file list (Wed Jan 8 22:33:26 2020)
  • compressing 2020.jan08.03e-1.0.mrc (Wed Jan 8 22:33:26 2020)
  • compressing 2020.jan08.03e-4.0.mrc (Wed Jan 8 22:33:26 2020)
  • compressing 2020.jan08.03e-7.0.mrc (Wed Jan 8 22:33:26 2020)
  • compressing 2020.jan08.03e-10.0.mrc (Wed Jan 8 22:33:26 2020)
  • FINISHED (Wed Jan 8 22:33:26 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/jan08/03e/2020.jan08.03e-10.0.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.jan08.03e-10.0.obj 
Message: UCSF Chimera completed in 5.62 sec 
OBJFILE /var/www/html/3vee/output/2020/jan08/03e/2020.jan08.03e-10.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-16.5, -0.6, 11.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 0.84 sec 
Message: compressing 2020.jan08.03e-10.0.mrc 
Message: tarring file list 
Message: compressing 2020.jan08.03e-1.0.mrc 
Message: compressing 2020.jan08.03e-4.0.mrc 
Message: compressing 2020.jan08.03e-7.0.mrc 
Message: compressing 2020.jan08.03e-10.0.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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