3v Running Log for JobId '2019.mar14.178'

Program is still running, progress is shown below

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  • host ip address=69.124.71.174 (Thu Mar 14 21:34:39 2019)
  • downloading pdb file (Thu Mar 14 21:34:39 2019)
  • failed to download pdb id: 1C4T (Thu Mar 14 21:34:39 2019)
  • trying download pdb id again without bio unit (Thu Mar 14 21:34:41 2019)
  • completed download of PDB id 1C4T (size: 450 k, 5683 lines) (Thu Mar 14 21:34:42 2019)
  • converting pdb into xyzr (Thu Mar 14 21:34:42 2019)
  • completed conversion of PDB file: 1C4T-2019.mar14.178.pdb (size: 156k) (Thu Mar 14 21:34:45 2019)
  • converted 4986 atoms of 4986 atoms (Thu Mar 14 21:34:45 2019)
  • found 4986 atoms in pdb (Thu Mar 14 21:34:45 2019)
  • running 3v solvent program (Thu Mar 14 21:34:45 2019)
  • imaging volume (download mrc) with UCSF Chimera (Thu Mar 14 21:34:47 2019)
  • UCSF Chimera created Jmol compatible file (Thu Mar 14 21:34:51 2019)
  • compressing 1C4T-2019.mar14.178.obj (Thu Mar 14 21:34:51 2019)
  • UCSF Chimera completed in 4.28 sec (Thu Mar 14 21:34:51 2019)
  • analyzing volume (Thu Mar 14 21:34:51 2019)
  • normal CoM (-24.1, -20.7, -4.8) Å (Thu Mar 14 21:34:55 2019)
  • reduced center failed (Thu Mar 14 21:34:55 2019)
  • volume analysis completed in 3.72 sec (Thu Mar 14 21:34:55 2019)
  • compressing 1C4T-2019.mar14.178.mrc (Thu Mar 14 21:34:55 2019)
  • FINISHED (Thu Mar 14 21:34:55 2019)

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Log file display

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Terminal display
		
Message: converting pdb into xyzr 
/srv/output/2019/mar14/178 
Message: completed conversion of PDB file: 1C4T-2019.mar14.178.pdb (size: 156k) 
Message: converted 4986 atoms of 4986 atoms 
Message: found 4986 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2019/mar14/178/1C4T-2019.mar14.178.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 1C4T-2019.mar14.178.obj 
Message: UCSF Chimera completed in 4.28 sec 
OBJFILE /var/www/html/3vee/output/2019/mar14/178/1C4T-2019.mar14.178.obj.gz 
Message: analyzing volume 
Message: normal CoM (-24.1, -20.7, -4.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 3.72 sec 
Message: compressing 1C4T-2019.mar14.178.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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