3v Running Log for JobId '2019.feb11.ff1'

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  • host ip address=77.80.52.226 (Mon Feb 11 03:41:55 2019)
  • converting pdb into xyzr (Mon Feb 11 03:41:55 2019)
  • completed conversion of PDB file: 2019.feb11.ff1.pdb (size: 89k) (Mon Feb 11 03:41:58 2019)
  • converted 2835 atoms of 2835 atoms (Mon Feb 11 03:41:58 2019)
  • found 2835 atoms in pdb (Mon Feb 11 03:41:58 2019)
  • running 3v volume program (Mon Feb 11 03:41:58 2019)
  • smoothing out volume (Mon Feb 11 03:57:52 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Feb 11 03:57:53 2019)
  • UCSF Chimera created Jmol compatible file (Mon Feb 11 03:58:00 2019)
  • compressing 2019.feb11.ff1.obj (Mon Feb 11 03:58:00 2019)
  • UCSF Chimera completed in 8.43 sec (Mon Feb 11 03:58:00 2019)
  • analyzing volume (Mon Feb 11 03:58:00 2019)
  • normal CoM (-16.3, 8.1, 16.0) Å (Mon Feb 11 03:58:50 2019)
  • reduced center failed (Mon Feb 11 03:58:58 2019)
  • volume analysis completed in 57.69 sec (Mon Feb 11 03:58:58 2019)
  • compressing 2019.feb11.ff1.mrc (Mon Feb 11 03:58:58 2019)
  • FINISHED (Mon Feb 11 03:58:58 2019)

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Log file display

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Terminal display
		
/srv/output/2019/feb11/ff1 
Message: completed conversion of PDB file: 2019.feb11.ff1.pdb (size: 89k) 
Message: converted 2835 atoms of 2835 atoms 
Message: found 2835 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/feb11/ff1/2019.feb11.ff1.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.feb11.ff1.obj 
Message: UCSF Chimera completed in 8.43 sec 
OBJFILE /var/www/html/3vee/output/2019/feb11/ff1/2019.feb11.ff1.obj.gz 
Message: analyzing volume 
Message: normal CoM (-16.3, 8.1, 16.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 57.69 sec 
Message: compressing 2019.feb11.ff1.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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