3v Running Log for JobId '2020.oct13.b07'

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  • host ip address=67.80.165.210 (Tue Oct 13 10:49:50 2020)
  • converting pdb into xyzr (Tue Oct 13 10:49:50 2020)
  • completed conversion of PDB file: 2020.oct13.b07.pdb (size: 548k) (Tue Oct 13 10:49:57 2020)
  • converted 17541 atoms of 17541 atoms (Tue Oct 13 10:49:57 2020)
  • found 17541 atoms in pdb (Tue Oct 13 10:49:57 2020)
  • running 3v solvent program (Tue Oct 13 10:49:57 2020)
  • imaging volume (download mrc) with UCSF Chimera (Tue Oct 13 10:50:35 2020)
  • UCSF Chimera created Jmol compatible file (Tue Oct 13 10:50:51 2020)
  • compressing 2020.oct13.b07.obj (Tue Oct 13 10:50:51 2020)
  • UCSF Chimera completed in 19.0 sec (Tue Oct 13 10:50:54 2020)
  • analyzing volume (Tue Oct 13 10:50:54 2020)
  • normal CoM (-33.5, 13.8, -8.8) Å (Tue Oct 13 10:51:35 2020)
  • reduced center failed (Tue Oct 13 10:51:42 2020)
  • volume analysis completed in 48.56 sec (Tue Oct 13 10:51:42 2020)
  • compressing 2020.oct13.b07.pdb (Tue Oct 13 10:51:42 2020)
  • compressing 2020.oct13.b07.mrc (Tue Oct 13 10:51:43 2020)
  • FINISHED (Tue Oct 13 10:51:44 2020)

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Log file display

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Terminal display
		
/srv/output/2020/oct13/b07 
Message: completed conversion of PDB file: 2020.oct13.b07.pdb (size: 548k) 
Message: converted 17541 atoms of 17541 atoms 
Message: found 17541 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2020/oct13/b07/2020.oct13.b07.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2020.oct13.b07.obj 
Message: UCSF Chimera completed in 19.0 sec 
OBJFILE /var/www/html/3vee/output/2020/oct13/b07/2020.oct13.b07.obj.gz 
Message: analyzing volume 
Message: normal CoM (-33.5, 13.8, -8.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 48.56 sec 
Message: compressing 2020.oct13.b07.pdb 
Message: compressing 2020.oct13.b07.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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