3v Running Log for JobId '2020.may20.b26'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=108.12.220.51 (Wed May 20 21:25:15 2020)
  • converting pdb into xyzr (Wed May 20 21:25:15 2020)
  • completed conversion of PDB file: 2020.may20.b26.pdb (size: 281k) (Wed May 20 21:25:22 2020)
  • converted 8980 atoms of 8980 atoms (Wed May 20 21:25:22 2020)
  • found 8980 atoms in pdb (Wed May 20 21:25:22 2020)
  • starting probe size 3.000 (Wed May 20 21:25:22 2020)
  • running 3v volume program (Wed May 20 21:25:22 2020)
  • smoothing out volume (Wed May 20 21:25:22 2020)
  • imaging volume (download mrc) with UCSF Chimera (Wed May 20 21:25:23 2020)
  • UCSF Chimera created Jmol compatible file (Wed May 20 21:25:34 2020)
  • compressing 2020.may20.b26-3.0.obj (Wed May 20 21:25:34 2020)
  • UCSF Chimera completed in 12.7 sec (Wed May 20 21:25:35 2020)
  • analyzing volume (Wed May 20 21:25:35 2020)
  • normal CoM (-6.6, 2.7, 16.9) Å (Wed May 20 21:25:46 2020)
  • reduced center failed (Wed May 20 21:25:48 2020)
  • volume analysis completed in 12.68 sec (Wed May 20 21:25:48 2020)
  • compressing 2020.may20.b26-3.0.mrc (Wed May 20 21:25:48 2020)
  • starting probe size 6.000 (Wed May 20 21:25:49 2020)
  • running 3v volume program (Wed May 20 21:25:49 2020)
  • smoothing out volume (Wed May 20 21:25:51 2020)
  • imaging volume (download mrc) with UCSF Chimera (Wed May 20 21:25:51 2020)
  • UCSF Chimera created Jmol compatible file (Wed May 20 21:26:03 2020)
  • compressing 2020.may20.b26-6.0.obj (Wed May 20 21:26:03 2020)
  • UCSF Chimera completed in 12.87 sec (Wed May 20 21:26:04 2020)
  • analyzing volume (Wed May 20 21:26:04 2020)
  • normal CoM (-6.7, 2.5, 16.8) Å (Wed May 20 21:26:16 2020)
  • reduced center failed (Wed May 20 21:26:19 2020)
  • volume analysis completed in 14.99 sec (Wed May 20 21:26:19 2020)
  • compressing 2020.may20.b26-6.0.mrc (Wed May 20 21:26:19 2020)
  • starting probe size 9.000 (Wed May 20 21:26:20 2020)
  • running 3v volume program (Wed May 20 21:26:20 2020)
  • smoothing out volume (Wed May 20 21:26:25 2020)
  • imaging volume (download mrc) with UCSF Chimera (Wed May 20 21:26:25 2020)
  • UCSF Chimera created Jmol compatible file (Wed May 20 21:26:37 2020)
  • compressing 2020.may20.b26-9.0.obj (Wed May 20 21:26:37 2020)
  • UCSF Chimera completed in 13.14 sec (Wed May 20 21:26:38 2020)
  • analyzing volume (Wed May 20 21:26:38 2020)
  • normal CoM (-6.7, 2.5, 16.9) Å (Wed May 20 21:26:52 2020)
  • reduced center failed (Wed May 20 21:26:56 2020)
  • volume analysis completed in 17.94 sec (Wed May 20 21:26:56 2020)
  • compressing 2020.may20.b26-9.0.mrc (Wed May 20 21:26:56 2020)
  • tarring file list (Wed May 20 21:26:57 2020)
  • compressing 2020.may20.b26-3.0.mrc (Wed May 20 21:26:57 2020)
  • compressing 2020.may20.b26-6.0.mrc (Wed May 20 21:26:57 2020)
  • compressing 2020.may20.b26-9.0.mrc (Wed May 20 21:26:57 2020)
  • FINISHED (Wed May 20 21:26:57 2020)

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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/2020/may20/b26/2020.may20.b26-9.0.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.may20.b26-9.0.obj 
Message: UCSF Chimera completed in 13.14 sec 
OBJFILE /var/www/html/3vee/output/2020/may20/b26/2020.may20.b26-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-6.7, 2.5, 16.9) Å 
Message: reduced center failed 
Message: volume analysis completed in 17.94 sec 
Message: compressing 2020.may20.b26-9.0.mrc 
Message: tarring file list 
Message: compressing 2020.may20.b26-3.0.mrc 
Message: compressing 2020.may20.b26-6.0.mrc 
Message: compressing 2020.may20.b26-9.0.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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