3v Running Log for JobId '2019.mar14.790'

Program is still running, progress is shown below

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  • host ip address=69.124.71.174 (Thu Mar 14 22:03:16 2019)
  • downloading pdb file (Thu Mar 14 22:03:17 2019)
  • failed to download pdb id: 1C4T (Thu Mar 14 22:03:17 2019)
  • trying download pdb id again without bio unit (Thu Mar 14 22:03:19 2019)
  • completed download of PDB id 1C4T (size: 450 k, 5683 lines) (Thu Mar 14 22:03:19 2019)
  • converting pdb into xyzr (Thu Mar 14 22:03:19 2019)
  • completed conversion of PDB file: 1C4T-2019.mar14.790.pdb (size: 156k) (Thu Mar 14 22:03:23 2019)
  • converted 4986 atoms of 4986 atoms (Thu Mar 14 22:03:23 2019)
  • found 4986 atoms in pdb (Thu Mar 14 22:03:23 2019)
  • running 3v all channel program (Thu Mar 14 22:03:23 2019)
  • created 1 channel files (Thu Mar 14 22:03:25 2019)
  • Download MRC files: 1 (Thu Mar 14 22:03:25 2019)
  • imaging volume (download mrc) with UCSF Chimera (Thu Mar 14 22:03:25 2019)
  • UCSF Chimera created Jmol compatible file (Thu Mar 14 22:03:28 2019)
  • compressing channel-001.obj (Thu Mar 14 22:03:28 2019)
  • UCSF Chimera completed in 3.67 sec (Thu Mar 14 22:03:29 2019)
  • analyzing volume (Thu Mar 14 22:03:29 2019)
  • normal CoM (-43.8, -48.8, -47.9) Å (Thu Mar 14 22:03:29 2019)
  • reduced center failed (Thu Mar 14 22:03:29 2019)
  • volume analysis completed in 16.85 msec (Thu Mar 14 22:03:29 2019)
  • compressing channel-001.mrc (Thu Mar 14 22:03:29 2019)
  • compressing channel-001.mrc (Thu Mar 14 22:03:29 2019)
  • FINISHED (Thu Mar 14 22:03:29 2019)

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Log file display

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Terminal display
		
Message: converted 4986 atoms of 4986 atoms 
Message: found 4986 atoms in pdb 
Message: running 3v all channel program 
Message: created 1 channel files 
Message: Download MRC files: 1 

Message: imaging volume (d ... 
himera/'>UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing channel-001.obj 
Message: UCSF Chimera completed in 3.67 sec 
OBJFILE /var/www/html/3vee/output/2019/mar14/790/channel-001.obj.gz 
Message: analyzing volume 
Message: normal CoM (-43.8, -48.8, -47.9) Å 
Message: reduced center failed 
Message: volume analysis completed in 16.85 msec 
Message: compressing channel-001.mrc 
Message: compressing channel-001.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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