3v Running Log for JobId '2019.jun27.c30'

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  • host ip address=165.89.84.89 (Thu Jun 27 09:54:33 2019)
  • converting pdb into xyzr (Thu Jun 27 09:54:33 2019)
  • completed conversion of PDB file: 2019.jun27.c30.pdb (size: 173k) (Thu Jun 27 09:54:37 2019)
  • converted 5540 atoms of 5540 atoms (Thu Jun 27 09:54:37 2019)
  • found 5540 atoms in pdb (Thu Jun 27 09:54:37 2019)
  • running 3v volume program (Thu Jun 27 09:54:37 2019)
  • smoothing out volume (Thu Jun 27 09:54:37 2019)
  • imaging volume (download mrc) with UCSF Chimera (Thu Jun 27 09:54:37 2019)
  • UCSF Chimera created Jmol compatible file (Thu Jun 27 09:54:43 2019)
  • compressing 2019.jun27.c30.obj (Thu Jun 27 09:54:43 2019)
  • UCSF Chimera completed in 6.14 sec (Thu Jun 27 09:54:43 2019)
  • analyzing volume (Thu Jun 27 09:54:43 2019)
  • normal CoM (-5.2, -14.2, 4.8) Å (Thu Jun 27 09:54:53 2019)
  • reduced center failed (Thu Jun 27 09:54:55 2019)
  • volume analysis completed in 11.31 sec (Thu Jun 27 09:54:55 2019)
  • compressing 2019.jun27.c30.mrc (Thu Jun 27 09:54:55 2019)
  • FINISHED (Thu Jun 27 09:54:55 2019)

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Log file display

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Terminal display
		
/srv/output/2019/jun27/c30 
Message: completed conversion of PDB file: 2019.jun27.c30.pdb (size: 173k) 
Message: converted 5540 atoms of 5540 atoms 
Message: found 5540 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/jun27/c30/2019.jun27.c30.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.jun27.c30.obj 
Message: UCSF Chimera completed in 6.14 sec 
OBJFILE /var/www/html/3vee/output/2019/jun27/c30/2019.jun27.c30.obj.gz 
Message: analyzing volume 
Message: normal CoM (-5.2, -14.2, 4.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 11.31 sec 
Message: compressing 2019.jun27.c30.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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