3v Running Log for JobId '2020.mar25.5e6'

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  • host ip address=14.139.160.235 (Thu Mar 26 01:22:51 2020)
  • converting pdb into xyzr (Thu Mar 26 01:22:51 2020)
  • completed conversion of PDB file: 2020.mar25.5e6.pdb (size: 75k) (Thu Mar 26 01:22:53 2020)
  • converted 2389 atoms of 2389 atoms (Thu Mar 26 01:22:53 2020)
  • found 2389 atoms in pdb (Thu Mar 26 01:22:53 2020)
  • running 3v volume program (Thu Mar 26 01:22:53 2020)
  • smoothing out volume (Thu Mar 26 01:22:53 2020)
  • imaging volume (download mrc) with UCSF Chimera (Thu Mar 26 01:22:53 2020)
  • UCSF Chimera created Jmol compatible file (Thu Mar 26 01:23:05 2020)
  • compressing 2020.mar25.5e6.obj (Thu Mar 26 01:23:05 2020)
  • UCSF Chimera completed in 11.68 sec (Thu Mar 26 01:23:05 2020)
  • analyzing volume (Thu Mar 26 01:23:05 2020)
  • normal CoM (3.0, -1.2, -1.3) Å (Thu Mar 26 01:23:06 2020)
  • reduced center failed (Thu Mar 26 01:23:06 2020)
  • volume analysis completed in 1.31 sec (Thu Mar 26 01:23:06 2020)
  • compressing 2020.mar25.5e6.mrc (Thu Mar 26 01:23:06 2020)
  • FINISHED (Thu Mar 26 01:23:06 2020)

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Log file display

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Terminal display
		
/srv/output/2020/mar25/5e6 
Message: completed conversion of PDB file: 2020.mar25.5e6.pdb (size: 75k) 
Message: converted 2389 atoms of 2389 atoms 
Message: found 2389 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2020/mar25/5e6/2020.mar25.5e6.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 2020.mar25.5e6.obj 
Message: UCSF Chimera completed in 11.68 sec 
OBJFILE /var/www/html/3vee/output/2020/mar25/5e6/2020.mar25.5e6.obj.gz 
Message: analyzing volume 
Message: normal CoM (3.0, -1.2, -1.3) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.31 sec 
Message: compressing 2020.mar25.5e6.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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