3v Running Log for JobId '2019.may15.c81'

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  • host ip address=193.61.207.162 (Wed May 15 13:03:16 2019)
  • converting pdb into xyzr (Wed May 15 13:03:16 2019)
  • completed conversion of PDB file: 2019.may15.c81.pdb (size: 31k) (Wed May 15 13:03:17 2019)
  • converted 994 atoms of 994 atoms (Wed May 15 13:03:17 2019)
  • found 994 atoms in pdb (Wed May 15 13:03:17 2019)
  • running 3v volume program (Wed May 15 13:03:17 2019)
  • smoothing out volume (Wed May 15 13:03:17 2019)
  • imaging volume (download mrc) with UCSF Chimera (Wed May 15 13:03:17 2019)
  • UCSF Chimera created Jmol compatible file (Wed May 15 13:03:28 2019)
  • compressing 2019.may15.c81.obj (Wed May 15 13:03:28 2019)
  • UCSF Chimera completed in 11.33 sec (Wed May 15 13:03:29 2019)
  • analyzing volume (Wed May 15 13:03:29 2019)
  • normal CoM (-3.8, -1.6, 3.0) Å (Wed May 15 13:03:30 2019)
  • reduced center failed (Wed May 15 13:03:31 2019)
  • volume analysis completed in 1.89 sec (Wed May 15 13:03:31 2019)
  • compressing 2019.may15.c81.pdb (Wed May 15 13:03:31 2019)
  • compressing 2019.may15.c81.mrc (Wed May 15 13:03:31 2019)
  • FINISHED (Wed May 15 13:03:31 2019)

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Log file display

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Terminal display
		
Message: completed conversion of PDB file: 2019.may15.c81.pdb (size: 31k) 
Message: converted 994 atoms of 994 atoms 
Message: found 994 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/may15/c81/2019.may15.c81.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 2019.may15.c81.obj 
Message: UCSF Chimera completed in 11.33 sec 
OBJFILE /var/www/html/3vee/output/2019/may15/c81/2019.may15.c81.obj.gz 
Message: analyzing volume 
Message: normal CoM (-3.8, -1.6, 3.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.89 sec 
Message: compressing 2019.may15.c81.pdb 
Message: compressing 2019.may15.c81.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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