3v Running Log for JobId '2017.oct12.726'

Program is still running, progress is shown below

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  • host ip address=160.80.35.224 (Thu Oct 12 06:35:38 2017)
  • downloading pdb file (Thu Oct 12 06:35:39 2017)
  • failed to download pdb id: 1GEI (Thu Oct 12 06:35:39 2017)
  • trying download pdb id again without bio unit (Thu Oct 12 06:35:41 2017)
  • completed download of PDB id 1GEI (size: 308 k, 3900 lines) (Thu Oct 12 06:35:41 2017)
  • converting pdb into xyzr (Thu Oct 12 06:35:41 2017)
  • completed conversion of PDB file: 1GEI-2017.oct12.726.pdb (size: 97k) (Thu Oct 12 06:35:44 2017)
  • converted 3099 atoms of 3099 atoms (Thu Oct 12 06:35:44 2017)
  • found 3099 atoms in pdb (Thu Oct 12 06:35:44 2017)
  • running 3v volume program (Thu Oct 12 06:35:44 2017)
  • smoothing out volume (Thu Oct 12 06:35:44 2017)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 12 06:35:44 2017)
  • UCSF Chimera created Jmol compatible file (Thu Oct 12 06:35:54 2017)
  • compressing 1GEI-2017.oct12.726.obj (Thu Oct 12 06:35:54 2017)
  • UCSF Chimera completed in 10.6 sec (Thu Oct 12 06:35:54 2017)
  • analyzing volume (Thu Oct 12 06:35:54 2017)
  • normal CoM (-5.8, -4.2, 4.8) Å (Thu Oct 12 06:35:56 2017)
  • reduced center failed (Thu Oct 12 06:35:56 2017)
  • volume analysis completed in 1.79 sec (Thu Oct 12 06:35:56 2017)
  • compressing 1GEI-2017.oct12.726.mrc (Thu Oct 12 06:35:56 2017)
  • FINISHED (Thu Oct 12 06:35:56 2017)

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Log file display

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Terminal display
		
/var/www/html/output/2017/oct12/726 
Message: completed conversion of PDB file: 1GEI-2017.oct12.726.pdb (size: 97k) 
Message: converted 3099 atoms of 3099 atoms 
Message: found 3099 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2017/oct12/726/1GEI-2017.oct12.726.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 1GEI-2017.oct12.726.obj 
Message: UCSF Chimera completed in 10.6 sec 
OBJFILE /var/www/html/3vee/output/2017/oct12/726/1GEI-2017.oct12.726.obj.gz 
Message: analyzing volume 
Message: normal CoM (-5.8, -4.2, 4.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.79 sec 
Message: compressing 1GEI-2017.oct12.726.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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