3v Running Log for JobId '2018.nov06.aed'

Program is still running, progress is shown below

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  • host ip address=130.219.10.90 (Tue Nov 6 16:55:58 2018)
  • downloading pdb file (Tue Nov 6 16:55:58 2018)
  • failed to download pdb id: 4aqs (Tue Nov 6 16:55:58 2018)
  • trying download pdb id again without bio unit (Tue Nov 6 16:56:00 2018)
  • completed download of PDB id 4aqs (size: 338 k, 4276 lines) (Tue Nov 6 16:56:00 2018)
  • converting pdb into xyzr (Tue Nov 6 16:56:00 2018)
  • completed conversion of PDB file: 4aqs-2018.nov06.aed.pdb (size: 110k) (Tue Nov 6 16:56:03 2018)
  • converted 3504 atoms of 3504 atoms (Tue Nov 6 16:56:03 2018)
  • found 3504 atoms in pdb (Tue Nov 6 16:56:03 2018)
  • running 3v volume program (Tue Nov 6 16:56:03 2018)
  • smoothing out volume (Tue Nov 6 16:56:03 2018)
  • imaging volume (download mrc) with UCSF Chimera (Tue Nov 6 16:56:03 2018)
  • UCSF Chimera created Jmol compatible file (Tue Nov 6 16:56:07 2018)
  • compressing 4aqs-2018.nov06.aed.obj (Tue Nov 6 16:56:07 2018)
  • UCSF Chimera completed in 4.15 sec (Tue Nov 6 16:56:07 2018)
  • analyzing volume (Tue Nov 6 16:56:07 2018)
  • normal CoM (-26.7, 0.7, 40.2) Å (Tue Nov 6 16:56:12 2018)
  • reduced center failed (Tue Nov 6 16:56:13 2018)
  • volume analysis completed in 5.11 sec (Tue Nov 6 16:56:13 2018)
  • compressing 4aqs-2018.nov06.aed.pdb (Tue Nov 6 16:56:13 2018)
  • compressing 4aqs-2018.nov06.aed.mrc (Tue Nov 6 16:56:13 2018)
  • FINISHED (Tue Nov 6 16:56:13 2018)

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Log file display

Show last lines of log file 
Terminal display
		
Message: completed conversion of PDB file: 4aqs-2018.nov06.aed.pdb (size: 110k) 
Message: converted 3504 atoms of 3504 atoms 
Message: found 3504 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2018/nov06/aed/4aqs-2018.nov06.aed.mrc 
Message: smoothing out volume 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 4aqs-2018.nov06.aed.obj 
Message: UCSF Chimera completed in 4.15 sec 
OBJFILE /var/www/html/3vee/output/2018/nov06/aed/4aqs-2018.nov06.aed.obj.gz 
Message: analyzing volume 
Message: normal CoM (-26.7, 0.7, 40.2) Å 
Message: reduced center failed 
Message: volume analysis completed in 5.11 sec 
Message: compressing 4aqs-2018.nov06.aed.pdb 
Message: compressing 4aqs-2018.nov06.aed.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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