3v Running Log for JobId '2020.oct15.474'

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  • host ip address=194.254.245.129 (Thu Oct 15 03:56:08 2020)
  • downloading pdb file (Thu Oct 15 03:56:08 2020)
  • failed to download pdb id: 4K3C (Thu Oct 15 03:56:08 2020)
  • trying download pdb id again without bio unit (Thu Oct 15 03:56:10 2020)
  • completed download of PDB id 4K3C (size: 668 k, 8448 lines) (Thu Oct 15 03:56:11 2020)
  • converting pdb into xyzr (Thu Oct 15 03:56:11 2020)
  • completed conversion of PDB file: 4K3C-2020.oct15.474.pdb (size: 123k) (Thu Oct 15 03:56:14 2020)
  • converted 3947 atoms of 3947 atoms (Thu Oct 15 03:56:14 2020)
  • found 3947 atoms in pdb (Thu Oct 15 03:56:14 2020)
  • running 3v all channel program (Thu Oct 15 03:56:14 2020)
  • created 2 channel files (Thu Oct 15 03:56:15 2020)
  • Download MRC files: 1 2 (Thu Oct 15 03:56:15 2020)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 15 03:56:15 2020)
  • UCSF Chimera created Jmol compatible file (Thu Oct 15 03:56:20 2020)
  • compressing channel-001.obj (Thu Oct 15 03:56:20 2020)
  • UCSF Chimera completed in 4.36 sec (Thu Oct 15 03:56:20 2020)
  • analyzing volume (Thu Oct 15 03:56:20 2020)
  • normal CoM (-41.4, -40.5, -68.9) Å (Thu Oct 15 03:56:20 2020)
  • reduced center failed (Thu Oct 15 03:56:20 2020)
  • volume analysis completed in 9.67 msec (Thu Oct 15 03:56:20 2020)
  • compressing channel-001.mrc (Thu Oct 15 03:56:20 2020)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 15 03:56:20 2020)
  • UCSF Chimera created Jmol compatible file (Thu Oct 15 03:56:25 2020)
  • compressing channel-002.obj (Thu Oct 15 03:56:25 2020)
  • UCSF Chimera completed in 5.31 sec (Thu Oct 15 03:56:25 2020)
  • analyzing volume (Thu Oct 15 03:56:25 2020)
  • normal CoM (-24.3, -33.2, -58.5) Å (Thu Oct 15 03:56:25 2020)
  • reduced center failed (Thu Oct 15 03:56:25 2020)
  • volume analysis completed in 170.99 msec (Thu Oct 15 03:56:25 2020)
  • compressing channel-002.mrc (Thu Oct 15 03:56:25 2020)
  • tarring file list (Thu Oct 15 03:56:25 2020)
  • compressing channel-001.mrc (Thu Oct 15 03:56:25 2020)
  • compressing channel-002.mrc (Thu Oct 15 03:56:25 2020)
  • FINISHED (Thu Oct 15 03:56:25 2020)

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Log file display

Show last lines of log file 
Terminal display
		
Message: reduced center failed 
Message: volume analysis completed in 9.67 msec 
Message: compressing channel-001.mrc 
Message: imaging volume (d ... 
himera/'>UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing channel-002.obj 
Message: UCSF Chimera completed in 5.31 sec 
OBJFILE /var/www/html/3vee/output/2020/oct15/474/channel-002.obj.gz 
Message: analyzing volume 
Message: normal CoM (-24.3, -33.2, -58.5) Å 
Message: reduced center failed 
Message: volume analysis completed in 170.99 msec 
Message: compressing channel-002.mrc 
Message: tarring file list 
Message: compressing channel-001.mrc 
Message: compressing channel-002.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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