3v Running Log for JobId '2022.jun22.e8a'

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  • host ip address=159.226.150.84 (Wed Jun 22 22:25:24 2022)
  • converting pdb into xyzr (Wed Jun 22 22:25:24 2022)
  • completed conversion of PDB file: 2022.jun22.e8a.pdb (size: 13k) (Wed Jun 22 22:25:25 2022)
  • converted 403 atoms of 403 atoms (Wed Jun 22 22:25:25 2022)
  • found 403 atoms in pdb (Wed Jun 22 22:25:25 2022)
  • running 3v all channel program (Wed Jun 22 22:25:25 2022)
  • created 1 channel files (Wed Jun 22 22:25:30 2022)
  • Download MRC files: 1 (Wed Jun 22 22:25:30 2022)
  • imaging volume (download mrc) with UCSF Chimera (Wed Jun 22 22:25:30 2022)
  • UCSF Chimera created Jmol compatible file (Wed Jun 22 22:25:32 2022)
  • compressing channel-001.obj (Wed Jun 22 22:25:32 2022)
  • UCSF Chimera completed in 2.54 sec (Wed Jun 22 22:25:33 2022)
  • analyzing volume (Wed Jun 22 22:25:33 2022)
  • normal CoM (-90.5, -24.5, -17.1) Å (Wed Jun 22 22:25:33 2022)
  • reduced center failed (Wed Jun 22 22:25:33 2022)
  • volume analysis completed in 167.81 msec (Wed Jun 22 22:25:33 2022)
  • compressing channel-001.mrc (Wed Jun 22 22:25:33 2022)
  • compressing channel-001.mrc (Wed Jun 22 22:25:33 2022)
  • FINISHED (Wed Jun 22 22:25:33 2022)

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Log file display

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Terminal display
		
Message: converted 403 atoms of 403 atoms 
Message: found 403 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 2.54 sec 
OBJFILE /var/www/html/3vee/output/2022/jun22/e8a/channel-001.obj.gz 
Message: analyzing volume 
Message: normal CoM (-90.5, -24.5, -17.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 167.81 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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