3v Running Log for JobId '2018.nov02.da7'

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  • host ip address=193.170.152.66 (Fri Nov 2 09:01:07 2018)
  • converting pdb into xyzr (Fri Nov 2 09:01:07 2018)
  • completed conversion of PDB file: 2018.nov02.da7.pdb (size: 4k) (Fri Nov 2 09:01:08 2018)
  • converted 141 atoms of 141 atoms (Fri Nov 2 09:01:08 2018)
  • found 141 atoms in pdb (Fri Nov 2 09:01:08 2018)
  • running 3v all channel program (Fri Nov 2 09:01:08 2018)
  • created 1 channel files (Fri Nov 2 09:01:08 2018)
  • Download MRC files: 1 (Fri Nov 2 09:01:08 2018)
  • imaging volume (download mrc) with UCSF Chimera (Fri Nov 2 09:01:08 2018)
  • UCSF Chimera created Jmol compatible file (Fri Nov 2 09:01:11 2018)
  • compressing channel-001.obj (Fri Nov 2 09:01:11 2018)
  • UCSF Chimera completed in 3.38 sec (Fri Nov 2 09:01:11 2018)
  • analyzing volume (Fri Nov 2 09:01:11 2018)
  • normal CoM (-22.8, -17.1, -8.3) Å (Fri Nov 2 09:01:12 2018)
  • reduced center failed (Fri Nov 2 09:01:12 2018)
  • volume analysis completed in 147.93 msec (Fri Nov 2 09:01:12 2018)
  • compressing channel-001.mrc (Fri Nov 2 09:01:12 2018)
  • compressing channel-001.mrc (Fri Nov 2 09:01:12 2018)
  • FINISHED (Fri Nov 2 09:01:12 2018)

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Log file display

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Terminal display
		
Message: converted 141 atoms of 141 atoms 
Message: found 141 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 3.38 sec 
OBJFILE /var/www/html/3vee/output/2018/nov02/da7/channel-001.obj.gz 
Message: analyzing volume 
Message: normal CoM (-22.8, -17.1, -8.3) Å 
Message: reduced center failed 
Message: volume analysis completed in 147.93 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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