3v Running Log for JobId '2019.dec02.0cf'

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  • host ip address=146.164.215.240 (Mon Dec 2 17:48:17 2019)
  • converting pdb into xyzr (Mon Dec 2 17:48:17 2019)
  • completed conversion of PDB file: 2019.dec02.0cf.pdb (size: 40k) (Mon Dec 2 17:48:18 2019)
  • converted 1270 atoms of 1270 atoms (Mon Dec 2 17:48:18 2019)
  • found 1270 atoms in pdb (Mon Dec 2 17:48:18 2019)
  • running 3v all channel program (Mon Dec 2 17:48:18 2019)
  • created 1 channel files (Mon Dec 2 17:48:18 2019)
  • Download MRC files: 1 (Mon Dec 2 17:48:18 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 17:48:18 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 17:48:21 2019)
  • compressing channel-001.obj (Mon Dec 2 17:48:21 2019)
  • UCSF Chimera completed in 2.79 sec (Mon Dec 2 17:48:21 2019)
  • analyzing volume (Mon Dec 2 17:48:21 2019)
  • normal CoM (-27.3, -20.9, -22.9) Å (Mon Dec 2 17:48:21 2019)
  • reduced center failed (Mon Dec 2 17:48:21 2019)
  • volume analysis completed in 32.53 msec (Mon Dec 2 17:48:21 2019)
  • compressing channel-001.mrc (Mon Dec 2 17:48:21 2019)
  • compressing channel-001.mrc (Mon Dec 2 17:48:21 2019)
  • FINISHED (Mon Dec 2 17:48:21 2019)

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Log file display

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Terminal display
		
Message: converted 1270 atoms of 1270 atoms 
Message: found 1270 atoms in pdb 
Message: running 3v all channel program 
Message: created 1 channel files 
Message: Download MRC files: 1 

Message: imaging volume (d ... 
himera/'>UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing channel-001.obj 
Message: UCSF Chimera completed in 2.79 sec 
OBJFILE /var/www/html/3vee/output/2019/dec02/0cf/channel-001.obj.gz 
Message: analyzing volume 
Message: normal CoM (-27.3, -20.9, -22.9) Å 
Message: reduced center failed 
Message: volume analysis completed in 32.53 msec 
Message: compressing channel-001.mrc 
Message: compressing channel-001.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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