3v Running Log for JobId '2019.jul11.6fd'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=64.54.0.183 (Thu Jul 11 18:11:22 2019)
  • downloading pdb file (Thu Jul 11 18:11:22 2019)
  • completed download of PDB id 2lyz (size: 130 k, 1648 lines) (Thu Jul 11 18:11:22 2019)
  • converting pdb into xyzr (Thu Jul 11 18:11:22 2019)
  • completed conversion of PDB file: 2lyz-2019.jul11.6fd.pdb (size: 31k) (Thu Jul 11 18:11:23 2019)
  • converted 1001 atoms of 1001 atoms (Thu Jul 11 18:11:23 2019)
  • found 1001 atoms in pdb (Thu Jul 11 18:11:23 2019)
  • running 3v solvent program (Thu Jul 11 18:11:23 2019)
  • imaging volume (download mrc) with UCSF Chimera (Thu Jul 11 18:11:24 2019)
  • UCSF Chimera created Jmol compatible file (Thu Jul 11 18:11:28 2019)
  • compressing 2lyz-2019.jul11.6fd.obj (Thu Jul 11 18:11:28 2019)
  • UCSF Chimera completed in 3.49 sec (Thu Jul 11 18:11:28 2019)
  • analyzing volume (Thu Jul 11 18:11:28 2019)
  • normal CoM (-13.8, -5.1, -15.6) Å (Thu Jul 11 18:11:32 2019)
  • reduced center failed (Thu Jul 11 18:11:32 2019)
  • volume analysis completed in 4.63 sec (Thu Jul 11 18:11:32 2019)
  • compressing 2lyz-2019.jul11.6fd.mrc (Thu Jul 11 18:11:32 2019)
  • FINISHED (Thu Jul 11 18:11:33 2019)

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Log file display

Show last lines of log file 
Terminal display
		
Message: converting pdb into xyzr 
/srv/output/2019/jul11/6fd 
Message: completed conversion of PDB file: 2lyz-2019.jul11.6fd.pdb (size: 31k) 
Message: converted 1001 atoms of 1001 atoms 
Message: found 1001 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2019/jul11/6fd/2lyz-2019.jul11.6fd.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2lyz-2019.jul11.6fd.obj 
Message: UCSF Chimera completed in 3.49 sec 
OBJFILE /var/www/html/3vee/output/2019/jul11/6fd/2lyz-2019.jul11.6fd.obj.gz 
Message: analyzing volume 
Message: normal CoM (-13.8, -5.1, -15.6) Å 
Message: reduced center failed 
Message: volume analysis completed in 4.63 sec 
Message: compressing 2lyz-2019.jul11.6fd.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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