3v Running Log for JobId '2021.feb22.3ad'

Program is still running, progress is shown below

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  • host ip address=130.60.168.9 (Mon Feb 22 16:48:19 2021)
  • downloading pdb file (Mon Feb 22 16:48:19 2021)
  • completed download of PDB id 6fnw (size: 892 k, 11275 lines) (Mon Feb 22 16:48:19 2021)
  • converting pdb into xyzr (Mon Feb 22 16:48:19 2021)
  • completed conversion of PDB file: 6fnw-2021.feb22.3ad.pdb (size: 219k) (Mon Feb 22 16:48:22 2021)
  • converted 7020 atoms of 7020 atoms (Mon Feb 22 16:48:22 2021)
  • found 7020 atoms in pdb (Mon Feb 22 16:48:22 2021)
  • running 3v volume program (Mon Feb 22 16:48:22 2021)
  • smoothing out volume (Mon Feb 22 16:48:22 2021)
  • imaging volume (download mrc) with UCSF Chimera (Mon Feb 22 16:48:22 2021)
  • UCSF Chimera created Jmol compatible file (Mon Feb 22 16:48:29 2021)
  • compressing 6fnw-2021.feb22.3ad.obj (Mon Feb 22 16:48:29 2021)
  • UCSF Chimera completed in 7.67 sec (Mon Feb 22 16:48:30 2021)
  • analyzing volume (Mon Feb 22 16:48:30 2021)
  • normal CoM (-2.0, -3.3, 1.1) Å (Mon Feb 22 16:48:32 2021)
  • reduced center failed (Mon Feb 22 16:48:32 2021)
  • volume analysis completed in 2.71 sec (Mon Feb 22 16:48:32 2021)
  • compressing 6fnw-2021.feb22.3ad.mrc (Mon Feb 22 16:48:32 2021)
  • FINISHED (Mon Feb 22 16:48:32 2021)

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Log file display

Show last lines of log file 
Terminal display
		
/srv/output/2021/feb22/3ad 
Message: completed conversion of PDB file: 6fnw-2021.feb22.3ad.pdb (size: 219k) 
Message: converted 7020 atoms of 7020 atoms 
Message: found 7020 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2021/feb22/3ad/6fnw-2021.feb22.3ad.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 6fnw-2021.feb22.3ad.obj 
Message: UCSF Chimera completed in 7.67 sec 
OBJFILE /var/www/html/3vee/output/2021/feb22/3ad/6fnw-2021.feb22.3ad.obj.gz 
Message: analyzing volume 
Message: normal CoM (-2.0, -3.3, 1.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 2.71 sec 
Message: compressing 6fnw-2021.feb22.3ad.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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