3v Running Log for JobId '2019.dec13.27e'

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  • host ip address=124.16.180.128 (Fri Dec 13 04:35:39 2019)
  • converting pdb into xyzr (Fri Dec 13 04:35:39 2019)
  • completed conversion of PDB file: 2019.dec13.27e.pdb (size: 11k) (Fri Dec 13 04:35:39 2019)
  • converted 360 atoms of 360 atoms (Fri Dec 13 04:35:39 2019)
  • found 360 atoms in pdb (Fri Dec 13 04:35:39 2019)
  • running 3v volume program (Fri Dec 13 04:35:39 2019)
  • smoothing out volume (Fri Dec 13 04:35:40 2019)
  • imaging volume (download mrc) with UCSF Chimera (Fri Dec 13 04:35:40 2019)
  • UCSF Chimera created Jmol compatible file (Fri Dec 13 04:35:45 2019)
  • compressing 2019.dec13.27e.obj (Fri Dec 13 04:35:45 2019)
  • UCSF Chimera completed in 5.46 sec (Fri Dec 13 04:35:45 2019)
  • analyzing volume (Fri Dec 13 04:35:45 2019)
  • normal CoM (-13.0, -2.6, 2.2) Å (Fri Dec 13 04:35:45 2019)
  • reduced center failed (Fri Dec 13 04:35:45 2019)
  • volume analysis completed in 348.12 msec (Fri Dec 13 04:35:45 2019)
  • compressing 2019.dec13.27e.mrc (Fri Dec 13 04:35:45 2019)
  • FINISHED (Fri Dec 13 04:35:45 2019)

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Log file display

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Terminal display
		
/srv/output/2019/dec13/27e 
Message: completed conversion of PDB file: 2019.dec13.27e.pdb (size: 11k) 
Message: converted 360 atoms of 360 atoms 
Message: found 360 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/dec13/27e/2019.dec13.27e.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.dec13.27e.obj 
Message: UCSF Chimera completed in 5.46 sec 
OBJFILE /var/www/html/3vee/output/2019/dec13/27e/2019.dec13.27e.obj.gz 
Message: analyzing volume 
Message: normal CoM (-13.0, -2.6, 2.2) Å 
Message: reduced center failed 
Message: volume analysis completed in 348.12 msec 
Message: compressing 2019.dec13.27e.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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