3v Running Log for JobId '2021.apr07.614'

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  • host ip address=146.57.128.236 (Wed Apr 7 19:54:00 2021)
  • converting pdb into xyzr (Wed Apr 7 19:54:00 2021)
  • completed conversion of PDB file: 2021.apr07.614.pdb (size: 1569k) (Wed Apr 7 19:55:35 2021)
  • converted 50213 atoms of 50213 atoms (Wed Apr 7 19:55:35 2021)
  • found 50213 atoms in pdb (Wed Apr 7 19:55:35 2021)
  • running 3v volume program (Wed Apr 7 19:55:35 2021)
  • smoothing out volume (Wed Apr 7 19:55:36 2021)
  • imaging volume (download mrc) with UCSF Chimera (Wed Apr 7 19:55:37 2021)
  • UCSF Chimera created Jmol compatible file (Wed Apr 7 19:55:40 2021)
  • compressing 2021.apr07.614.obj (Wed Apr 7 19:55:40 2021)
  • UCSF Chimera completed in 4.45 sec (Wed Apr 7 19:55:40 2021)
  • analyzing volume (Wed Apr 7 19:55:40 2021)
  • normal CoM (-433.4, 29.7, 464.7) Å (Wed Apr 7 19:56:17 2021)
  • reduced center failed (Wed Apr 7 19:56:21 2021)
  • volume analysis completed in 40.98 sec (Wed Apr 7 19:56:21 2021)
  • compressing 2021.apr07.614.mrc (Wed Apr 7 19:56:21 2021)
  • FINISHED (Wed Apr 7 19:56:22 2021)

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Log file display

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Terminal display
		
/srv/output/2021/apr07/614 
Message: completed conversion of PDB file: 2021.apr07.614.pdb (size: 1569k) 
Message: converted 50213 atoms of 50213 atoms 
Message: found 50213 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2021/apr07/614/2021.apr07.614.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.apr07.614.obj 
Message: UCSF Chimera completed in 4.45 sec 
OBJFILE /var/www/html/3vee/output/2021/apr07/614/2021.apr07.614.obj.gz 
Message: analyzing volume 
Message: normal CoM (-433.4, 29.7, 464.7) Å 
Message: reduced center failed 
Message: volume analysis completed in 40.98 sec 
Message: compressing 2021.apr07.614.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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