3v Running Log for JobId '2022.may13.0e5'

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  • host ip address=157.0.207.64 (Fri May 13 10:54:47 2022)
  • converting pdb into xyzr (Fri May 13 10:54:47 2022)
  • completed conversion of PDB file: 2022.may13.0e5.pdb (size: 16k) (Fri May 13 10:54:47 2022)
  • converted 496 atoms of 496 atoms (Fri May 13 10:54:47 2022)
  • found 496 atoms in pdb (Fri May 13 10:54:47 2022)
  • running 3v volume program (Fri May 13 10:54:47 2022)
  • smoothing out volume (Fri May 13 10:54:47 2022)
  • imaging volume (download mrc) with UCSF Chimera (Fri May 13 10:54:47 2022)
  • UCSF Chimera created Jmol compatible file (Fri May 13 10:54:53 2022)
  • compressing 2022.may13.0e5.obj (Fri May 13 10:54:53 2022)
  • UCSF Chimera completed in 5.93 sec (Fri May 13 10:54:53 2022)
  • analyzing volume (Fri May 13 10:54:53 2022)
  • normal CoM (3.1, -4.7, -5.8) Å (Fri May 13 10:54:54 2022)
  • reduced center failed (Fri May 13 10:54:54 2022)
  • volume analysis completed in 481.42 msec (Fri May 13 10:54:54 2022)
  • compressing 2022.may13.0e5.mrc (Fri May 13 10:54:54 2022)
  • FINISHED (Fri May 13 10:54:54 2022)

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Log file display

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Terminal display
		
/srv/output/2022/may13/0e5 
Message: completed conversion of PDB file: 2022.may13.0e5.pdb (size: 16k) 
Message: converted 496 atoms of 496 atoms 
Message: found 496 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2022/may13/0e5/2022.may13.0e5.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 2022.may13.0e5.obj 
Message: UCSF Chimera completed in 5.93 sec 
OBJFILE /var/www/html/3vee/output/2022/may13/0e5/2022.may13.0e5.obj.gz 
Message: analyzing volume 
Message: normal CoM (3.1, -4.7, -5.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 481.42 msec 
Message: compressing 2022.may13.0e5.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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