3v Running Log for JobId '2022.jun22.1c3'

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  • host ip address=159.226.150.84 (Wed Jun 22 22:36:38 2022)
  • converting pdb into xyzr (Wed Jun 22 22:36:38 2022)
  • completed conversion of PDB file: 2022.jun22.1c3.pdb (size: 5k) (Wed Jun 22 22:36:38 2022)
  • converted 150 atoms of 150 atoms (Wed Jun 22 22:36:38 2022)
  • found 150 atoms in pdb (Wed Jun 22 22:36:38 2022)
  • running 3v all channel program (Wed Jun 22 22:36:38 2022)
  • created 1 channel files (Wed Jun 22 22:36:40 2022)
  • Download MRC files: 1 (Wed Jun 22 22:36:40 2022)
  • imaging volume (download mrc) with UCSF Chimera (Wed Jun 22 22:36:40 2022)
  • UCSF Chimera created Jmol compatible file (Wed Jun 22 22:36:43 2022)
  • compressing channel-001.obj (Wed Jun 22 22:36:43 2022)
  • UCSF Chimera completed in 3.11 sec (Wed Jun 22 22:36:43 2022)
  • analyzing volume (Wed Jun 22 22:36:43 2022)
  • normal CoM (-17.3, -14.9, -16.5) Å (Wed Jun 22 22:36:44 2022)
  • reduced center failed (Wed Jun 22 22:36:44 2022)
  • volume analysis completed in 138.55 msec (Wed Jun 22 22:36:44 2022)
  • compressing channel-001.mrc (Wed Jun 22 22:36:44 2022)
  • compressing channel-001.mrc (Wed Jun 22 22:36:44 2022)
  • FINISHED (Wed Jun 22 22:36:44 2022)

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Log file display

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Terminal display
		
Message: converted 150 atoms of 150 atoms 
Message: found 150 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 3.11 sec 
OBJFILE /var/www/html/3vee/output/2022/jun22/1c3/channel-001.obj.gz 
Message: analyzing volume 
Message: normal CoM (-17.3, -14.9, -16.5) Å 
Message: reduced center failed 
Message: volume analysis completed in 138.55 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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