3v Running Log for JobId '2019.oct09.7cd'

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  • host ip address=200.44.94.188 (Wed Oct 9 22:02:14 2019)
  • converting pdb into xyzr (Wed Oct 9 22:02:14 2019)
  • completed conversion of PDB file: 2019.oct09.7cd.pdb (size: 1306k) (Wed Oct 9 22:02:29 2019)
  • converted 41797 atoms of 41797 atoms (Wed Oct 9 22:02:29 2019)
  • found 41797 atoms in pdb (Wed Oct 9 22:02:29 2019)
  • running 3v volume program (Wed Oct 9 22:02:29 2019)
  • smoothing out volume (Wed Oct 9 22:02:30 2019)
  • imaging volume (download mrc) with UCSF Chimera (Wed Oct 9 22:02:30 2019)
  • UCSF Chimera created Jmol compatible file (Wed Oct 9 22:02:42 2019)
  • compressing 2019.oct09.7cd.obj (Wed Oct 9 22:02:42 2019)
  • UCSF Chimera completed in 13.36 sec (Wed Oct 9 22:02:43 2019)
  • analyzing volume (Wed Oct 9 22:02:43 2019)
  • normal CoM (31.2, 4.5, -31.5) Å (Wed Oct 9 22:02:56 2019)
  • reduced center failed (Wed Oct 9 22:02:58 2019)
  • volume analysis completed in 14.65 sec (Wed Oct 9 22:02:58 2019)
  • compressing 2019.oct09.7cd.mrc (Wed Oct 9 22:02:58 2019)
  • FINISHED (Wed Oct 9 22:02:59 2019)

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Log file display

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Terminal display
		
/srv/output/2019/oct09/7cd 
Message: completed conversion of PDB file: 2019.oct09.7cd.pdb (size: 1306k) 
Message: converted 41797 atoms of 41797 atoms 
Message: found 41797 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/oct09/7cd/2019.oct09.7cd.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.oct09.7cd.obj 
Message: UCSF Chimera completed in 13.36 sec 
OBJFILE /var/www/html/3vee/output/2019/oct09/7cd/2019.oct09.7cd.obj.gz 
Message: analyzing volume 
Message: normal CoM (31.2, 4.5, -31.5) Å 
Message: reduced center failed 
Message: volume analysis completed in 14.65 sec 
Message: compressing 2019.oct09.7cd.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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