3v Running Log for JobId '2021.jan13.4e7'

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  • host ip address=85.144.225.97 (Wed Jan 13 07:38:17 2021)
  • converting pdb into xyzr (Wed Jan 13 07:38:17 2021)
  • completed conversion of PDB file: 2021.jan13.4e7.pdb (size: 242k) (Wed Jan 13 07:38:30 2021)
  • converted 7745 atoms of 7745 atoms (Wed Jan 13 07:38:30 2021)
  • found 7745 atoms in pdb (Wed Jan 13 07:38:30 2021)
  • running 3v volume program (Wed Jan 13 07:38:30 2021)
  • smoothing out volume (Wed Jan 13 07:38:31 2021)
  • imaging volume (download mrc) with UCSF Chimera (Wed Jan 13 07:38:31 2021)
  • UCSF Chimera created Jmol compatible file (Wed Jan 13 07:38:48 2021)
  • compressing 2021.jan13.4e7.obj (Wed Jan 13 07:38:48 2021)
  • UCSF Chimera completed in 17.68 sec (Wed Jan 13 07:38:49 2021)
  • analyzing volume (Wed Jan 13 07:38:49 2021)
  • normal CoM (-4.5, -2.9, 1.5) Å (Wed Jan 13 07:38:57 2021)
  • reduced center failed (Wed Jan 13 07:38:58 2021)
  • volume analysis completed in 9.33 sec (Wed Jan 13 07:38:58 2021)
  • compressing 2021.jan13.4e7.mrc (Wed Jan 13 07:38:58 2021)
  • FINISHED (Wed Jan 13 07:38:58 2021)

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Log file display

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Terminal display
		
/srv/output/2021/jan13/4e7 
Message: completed conversion of PDB file: 2021.jan13.4e7.pdb (size: 242k) 
Message: converted 7745 atoms of 7745 atoms 
Message: found 7745 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2021/jan13/4e7/2021.jan13.4e7.mrc 
Message: smoothing out volume 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2021.jan13.4e7.obj 
Message: UCSF Chimera completed in 17.68 sec 
OBJFILE /var/www/html/3vee/output/2021/jan13/4e7/2021.jan13.4e7.obj.gz 
Message: analyzing volume 
Message: normal CoM (-4.5, -2.9, 1.5) Å 
Message: reduced center failed 
Message: volume analysis completed in 9.33 sec 
Message: compressing 2021.jan13.4e7.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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