3v Running Log for JobId '2021.apr07.fcf'

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  • host ip address=98.247.86.204 (Wed Apr 7 13:37:16 2021)
  • converting pdb into xyzr (Wed Apr 7 13:37:17 2021)
  • completed conversion of PDB file: 2021.apr07.fcf.pdb (size: 73k) (Wed Apr 7 13:37:17 2021)
  • converted 2326 atoms of 2326 atoms (Wed Apr 7 13:37:17 2021)
  • found 2326 atoms in pdb (Wed Apr 7 13:37:17 2021)
  • running 3v solvent program (Wed Apr 7 13:37:17 2021)
  • imaging volume (download mrc) with UCSF Chimera (Wed Apr 7 13:37:18 2021)
  • UCSF Chimera created Jmol compatible file (Wed Apr 7 13:37:22 2021)
  • compressing 2021.apr07.fcf.obj (Wed Apr 7 13:37:22 2021)
  • UCSF Chimera completed in 3.61 sec (Wed Apr 7 13:37:22 2021)
  • analyzing volume (Wed Apr 7 13:37:22 2021)
  • normal CoM (-9.4, -2.4, 10.6) Å (Wed Apr 7 13:37:23 2021)
  • reduced center failed (Wed Apr 7 13:37:23 2021)
  • volume analysis completed in 1.48 sec (Wed Apr 7 13:37:23 2021)
  • compressing 2021.apr07.fcf.mrc (Wed Apr 7 13:37:23 2021)
  • FINISHED (Wed Apr 7 13:37:23 2021)

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Log file display

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Terminal display
		
Message: converting pdb into xyzr 
/srv/output/2021/apr07/fcf 
Message: completed conversion of PDB file: 2021.apr07.fcf.pdb (size: 73k) 
Message: converted 2326 atoms of 2326 atoms 
Message: found 2326 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2021/apr07/fcf/2021.apr07.fcf.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2021.apr07.fcf.obj 
Message: UCSF Chimera completed in 3.61 sec 
OBJFILE /var/www/html/3vee/output/2021/apr07/fcf/2021.apr07.fcf.obj.gz 
Message: analyzing volume 
Message: normal CoM (-9.4, -2.4, 10.6) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.48 sec 
Message: compressing 2021.apr07.fcf.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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