3v Running Log for JobId '2018.may16.a60'

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  • host ip address=218.3.243.80 (Wed May 16 09:39:47 2018)
  • converting pdb into xyzr (Wed May 16 09:39:48 2018)
  • completed conversion of PDB file: 2018.may16.a60.pdb (size: 312k) (Wed May 16 09:39:59 2018)
  • converted 9999 atoms of 12602 atoms (Wed May 16 09:39:59 2018)
  • found 9999 atoms in pdb (Wed May 16 09:39:59 2018)
  • running 3v solvent program (Wed May 16 09:39:59 2018)
  • imaging volume (download mrc) with UCSF Chimera (Wed May 16 09:40:38 2018)
  • UCSF Chimera created Jmol compatible file (Wed May 16 09:41:17 2018)
  • compressing 2018.may16.a60.obj (Wed May 16 09:41:17 2018)
  • UCSF Chimera completed in 43.85 sec (Wed May 16 09:41:22 2018)
  • analyzing volume (Wed May 16 09:41:22 2018)
  • normal CoM (-22.0, -1.2, -1.2) Å (Wed May 16 09:41:47 2018)
  • reduced center failed (Wed May 16 09:41:53 2018)
  • volume analysis completed in 30.88 sec (Wed May 16 09:41:53 2018)
  • compressing 2018.may16.a60.mrc (Wed May 16 09:41:53 2018)
  • FINISHED (Wed May 16 09:41:53 2018)

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Log file display

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Terminal display
		
Message: converting pdb into xyzr 
/var/www/html/output/2018/may16/a60 
Message: completed conversion of PDB file: 2018.may16.a60.pdb (size: 312k) 
Message: converted 9999 atoms of 12602 atoms 
Message: found 9999 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2018/may16/a60/2018.may16.a60.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2018.may16.a60.obj 
Message: UCSF Chimera completed in 43.85 sec 
OBJFILE /var/www/html/3vee/output/2018/may16/a60/2018.may16.a60.obj.gz 
Message: analyzing volume 
Message: normal CoM (-22.0, -1.2, -1.2) Å 
Message: reduced center failed 
Message: volume analysis completed in 30.88 sec 
Message: compressing 2018.may16.a60.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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