3v Running Log for JobId '2019.jan10.17f'

Program is still running, progress is shown below

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  • host ip address=14.139.220.33 (Thu Jan 10 07:11:11 2019)
  • downloading pdb file (Thu Jan 10 07:11:11 2019)
  • failed to download pdb id: 4ptx (Thu Jan 10 07:11:11 2019)
  • trying download pdb id again without bio unit (Thu Jan 10 07:11:13 2019)
  • completed download of PDB id 4ptx (size: 1252 k, 15825 lines) (Thu Jan 10 07:11:14 2019)
  • converting pdb into xyzr (Thu Jan 10 07:11:14 2019)
  • completed conversion of PDB file: 4ptx-2019.jan10.17f.pdb (size: 229k) (Thu Jan 10 07:11:19 2019)
  • converted 7316 atoms of 7316 atoms (Thu Jan 10 07:11:19 2019)
  • found 7316 atoms in pdb (Thu Jan 10 07:11:19 2019)
  • running 3v volume program (Thu Jan 10 07:11:19 2019)
  • smoothing out volume (Thu Jan 10 07:11:20 2019)
  • imaging volume (download mrc) with UCSF Chimera (Thu Jan 10 07:11:20 2019)
  • UCSF Chimera created Jmol compatible file (Thu Jan 10 07:11:28 2019)
  • compressing 4ptx-2019.jan10.17f.obj (Thu Jan 10 07:11:28 2019)
  • UCSF Chimera completed in 8.83 sec (Thu Jan 10 07:11:28 2019)
  • analyzing volume (Thu Jan 10 07:11:28 2019)
  • normal CoM (-17.9, 0.9, 13.1) Å (Thu Jan 10 07:11:32 2019)
  • reduced center failed (Thu Jan 10 07:11:33 2019)
  • volume analysis completed in 4.41 sec (Thu Jan 10 07:11:33 2019)
  • compressing 4ptx-2019.jan10.17f.mrc (Thu Jan 10 07:11:33 2019)
  • FINISHED (Thu Jan 10 07:11:33 2019)

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Log file display

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Terminal display
		
/srv/output/2019/jan10/17f 
Message: completed conversion of PDB file: 4ptx-2019.jan10.17f.pdb (size: 229k) 
Message: converted 7316 atoms of 7316 atoms 
Message: found 7316 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/jan10/17f/4ptx-2019.jan10.17f.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 4ptx-2019.jan10.17f.obj 
Message: UCSF Chimera completed in 8.83 sec 
OBJFILE /var/www/html/3vee/output/2019/jan10/17f/4ptx-2019.jan10.17f.obj.gz 
Message: analyzing volume 
Message: normal CoM (-17.9, 0.9, 13.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 4.41 sec 
Message: compressing 4ptx-2019.jan10.17f.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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