3v Running Log for JobId '2020.may18.2d8'

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  • host ip address=165.225.194.209 (Mon May 18 07:27:29 2020)
  • converting pdb into xyzr (Mon May 18 07:27:29 2020)
  • completed conversion of PDB file: 2020.may18.2d8.pdb (size: 117k) (Mon May 18 07:27:32 2020)
  • converted 3754 atoms of 3754 atoms (Mon May 18 07:27:32 2020)
  • found 3754 atoms in pdb (Mon May 18 07:27:32 2020)
  • running 3v volume program (Mon May 18 07:27:32 2020)
  • smoothing out volume (Mon May 18 07:27:34 2020)
  • imaging volume (download mrc) with UCSF Chimera (Mon May 18 07:27:34 2020)
  • UCSF Chimera created Jmol compatible file (Mon May 18 07:27:44 2020)
  • compressing 2020.may18.2d8.obj (Mon May 18 07:27:44 2020)
  • UCSF Chimera completed in 11.56 sec (Mon May 18 07:27:45 2020)
  • analyzing volume (Mon May 18 07:27:45 2020)
  • normal CoM (-4.8, 0.4, 0.3) Å (Mon May 18 07:27:57 2020)
  • reduced center failed (Mon May 18 07:28:00 2020)
  • volume analysis completed in 14.59 sec (Mon May 18 07:28:00 2020)
  • compressing 2020.may18.2d8.pdb (Mon May 18 07:28:00 2020)
  • compressing 2020.may18.2d8.mrc (Mon May 18 07:28:01 2020)
  • FINISHED (Mon May 18 07:28:01 2020)

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Log file display

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Terminal display
		
Message: completed conversion of PDB file: 2020.may18.2d8.pdb (size: 117k) 
Message: converted 3754 atoms of 3754 atoms 
Message: found 3754 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2020/may18/2d8/2020.may18.2d8.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.may18.2d8.obj 
Message: UCSF Chimera completed in 11.56 sec 
OBJFILE /var/www/html/3vee/output/2020/may18/2d8/2020.may18.2d8.obj.gz 
Message: analyzing volume 
Message: normal CoM (-4.8, 0.4, 0.3) Å 
Message: reduced center failed 
Message: volume analysis completed in 14.59 sec 
Message: compressing 2020.may18.2d8.pdb 
Message: compressing 2020.may18.2d8.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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