3v Running Log for JobId '2017.mar13.edb'

Program is still running, progress is shown below

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  • host ip address=89.128.164.9 (Mon Mar 13 10:45:24 2017)
  • converting pdb into xyzr (Mon Mar 13 10:45:24 2017)
  • completed conversion of PDB file: 2017.mar13.edb.pdb (size: 50k) (Mon Mar 13 10:45:26 2017)
  • converted 1612 atoms of 1612 atoms (Mon Mar 13 10:45:26 2017)
  • found 1612 atoms in pdb (Mon Mar 13 10:45:26 2017)
  • running 3v solvent program (Mon Mar 13 10:45:26 2017)
  • imaging volume (download mrc) with UCSF Chimera (Mon Mar 13 10:45:33 2017)
  • UCSF Chimera created Jmol compatible file (Mon Mar 13 10:45:51 2017)
  • compressing 2017.mar13.edb.obj (Mon Mar 13 10:45:51 2017)
  • UCSF Chimera completed in 21.33 sec (Mon Mar 13 10:45:55 2017)
  • analyzing volume (Mon Mar 13 10:45:55 2017)
  • normal CoM (-1.6, -0.3, 0.8) Å (Mon Mar 13 10:46:06 2017)
  • reduced center failed (Mon Mar 13 10:46:08 2017)
  • volume analysis completed in 13.07 sec (Mon Mar 13 10:46:08 2017)
  • compressing 2017.mar13.edb.mrc (Mon Mar 13 10:46:08 2017)
  • FINISHED (Mon Mar 13 10:46:08 2017)

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Log file display

Show last lines of log file 
Terminal display
		
Message: converting pdb into xyzr 
/var/www/html/output/2017/mar13/edb 
Message: completed conversion of PDB file: 2017.mar13.edb.pdb (size: 50k) 
Message: converted 1612 atoms of 1612 atoms 
Message: found 1612 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2017/mar13/edb/2017.mar13.edb.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2017.mar13.edb.obj 
Message: UCSF Chimera completed in 21.33 sec 
OBJFILE /var/www/html/3vee/output/2017/mar13/edb/2017.mar13.edb.obj.gz 
Message: analyzing volume 
Message: normal CoM (-1.6, -0.3, 0.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 13.07 sec 
Message: compressing 2017.mar13.edb.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] yahoo.com>
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