3v Running Log for JobId '2019.oct07.8cb'

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  • host ip address=193.147.148.112 (Mon Oct 7 06:41:18 2019)
  • converting pdb into xyzr (Mon Oct 7 06:41:18 2019)
  • completed conversion of PDB file: 2019.oct07.8cb.pdb (size: 845k) (Mon Oct 7 06:41:28 2019)
  • converted 27055 atoms of 27055 atoms (Mon Oct 7 06:41:28 2019)
  • found 27055 atoms in pdb (Mon Oct 7 06:41:28 2019)
  • running 3v all channel program (Mon Oct 7 06:41:28 2019)
  • created 1 channel files (Mon Oct 7 06:41:35 2019)
  • Download MRC files: 1 (Mon Oct 7 06:41:35 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Oct 7 06:41:35 2019)
  • UCSF Chimera created Jmol compatible file (Mon Oct 7 06:41:45 2019)
  • compressing channel-001.obj (Mon Oct 7 06:41:45 2019)
  • UCSF Chimera completed in 10.4 sec (Mon Oct 7 06:41:46 2019)
  • analyzing volume (Mon Oct 7 06:41:46 2019)
  • normal CoM (-44.9, -40.9, -37.1) Å (Mon Oct 7 06:41:46 2019)
  • reduced center failed (Mon Oct 7 06:41:46 2019)
  • volume analysis completed in 471.15 msec (Mon Oct 7 06:41:46 2019)
  • compressing channel-001.mrc (Mon Oct 7 06:41:46 2019)
  • compressing channel-001.mrc (Mon Oct 7 06:41:46 2019)
  • FINISHED (Mon Oct 7 06:41:46 2019)

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Log file display

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Terminal display
		
Message: converted 27055 atoms of 27055 atoms 
Message: found 27055 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 10.4 sec 
OBJFILE /var/www/html/3vee/output/2019/oct07/8cb/channel-001.obj.gz 
Message: analyzing volume 
Message: normal CoM (-44.9, -40.9, -37.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 471.15 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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