3v Running Log for JobId '2018.mar13.799'

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  • host ip address=85.211.26.33 (Tue Mar 13 13:44:02 2018)
  • converting pdb into xyzr (Tue Mar 13 13:44:03 2018)
  • completed conversion of PDB file: 2018.mar13.799.pdb (size: 49k) (Tue Mar 13 13:44:04 2018)
  • converted 1557 atoms of 1557 atoms (Tue Mar 13 13:44:04 2018)
  • found 1557 atoms in pdb (Tue Mar 13 13:44:04 2018)
  • running 3v all channel program (Tue Mar 13 13:44:04 2018)
  • created 1 channel files (Tue Mar 13 13:44:04 2018)
  • Download MRC files: 1 (Tue Mar 13 13:44:04 2018)
  • imaging volume (download mrc) with UCSF Chimera (Tue Mar 13 13:44:04 2018)
  • UCSF Chimera created Jmol compatible file (Tue Mar 13 13:44:07 2018)
  • compressing channel-001.obj (Tue Mar 13 13:44:07 2018)
  • UCSF Chimera completed in 2.93 sec (Tue Mar 13 13:44:07 2018)
  • analyzing volume (Tue Mar 13 13:44:07 2018)
  • normal CoM (-26.3, -24.7, -31.9) Å (Tue Mar 13 13:44:07 2018)
  • reduced center failed (Tue Mar 13 13:44:07 2018)
  • volume analysis completed in 21.53 msec (Tue Mar 13 13:44:07 2018)
  • compressing channel-001.mrc (Tue Mar 13 13:44:07 2018)
  • compressing channel-001.mrc (Tue Mar 13 13:44:07 2018)
  • FINISHED (Tue Mar 13 13:44:07 2018)

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Log file display

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Terminal display
		
Message: converted 1557 atoms of 1557 atoms 
Message: found 1557 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 2.93 sec 
OBJFILE /var/www/html/3vee/output/2018/mar13/799/channel-001.obj.gz 
Message: analyzing volume 
Message: normal CoM (-26.3, -24.7, -31.9) Å 
Message: reduced center failed 
Message: volume analysis completed in 21.53 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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