3v Running Log for JobId '2021.apr07.4c7'

Program is still running, progress is shown below

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  • host ip address=98.247.86.204 (Wed Apr 7 13:18:52 2021)
  • downloading pdb file (Wed Apr 7 13:18:52 2021)
  • completed download of PDB id 2oar (size: 389 k, 4914 lines) (Wed Apr 7 13:18:54 2021)
  • converting pdb into xyzr (Wed Apr 7 13:18:54 2021)
  • completed conversion of PDB file: 2oar-2021.apr07.4c7.pdb (size: 149k) (Wed Apr 7 13:18:57 2021)
  • converted 4755 atoms of 4755 atoms (Wed Apr 7 13:18:57 2021)
  • found 4755 atoms in pdb (Wed Apr 7 13:18:57 2021)
  • running 3v all channel program (Wed Apr 7 13:18:57 2021)
  • created 1 channel files (Wed Apr 7 13:19:01 2021)
  • Download MRC files: 1 (Wed Apr 7 13:19:01 2021)
  • imaging volume (download mrc) with UCSF Chimera (Wed Apr 7 13:19:01 2021)
  • UCSF Chimera created Jmol compatible file (Wed Apr 7 13:19:05 2021)
  • compressing channel-001.obj (Wed Apr 7 13:19:05 2021)
  • UCSF Chimera completed in 4.56 sec (Wed Apr 7 13:19:05 2021)
  • analyzing volume (Wed Apr 7 13:19:05 2021)
  • normal CoM (-40.7, -39.5, -25.7) Å (Wed Apr 7 13:19:05 2021)
  • reduced center failed (Wed Apr 7 13:19:05 2021)
  • volume analysis completed in 352.87 msec (Wed Apr 7 13:19:05 2021)
  • compressing channel-001.mrc (Wed Apr 7 13:19:05 2021)
  • compressing channel-001.mrc (Wed Apr 7 13:19:05 2021)
  • FINISHED (Wed Apr 7 13:19:05 2021)

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Log file display

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Terminal display
		
Message: converted 4755 atoms of 4755 atoms 
Message: found 4755 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 4.56 sec 
OBJFILE /var/www/html/3vee/output/2021/apr07/4c7/channel-001.obj.gz 
Message: analyzing volume 
Message: normal CoM (-40.7, -39.5, -25.7) Å 
Message: reduced center failed 
Message: volume analysis completed in 352.87 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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