3v Running Log for JobId '2018.feb09.841'

Program is still running, progress is shown below

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  • host ip address=94.6.220.247 (Fri Feb 9 06:36:23 2018)
  • downloading pdb file (Fri Feb 9 06:36:23 2018)
  • failed to download pdb id: 3o9p (Fri Feb 9 06:36:23 2018)
  • trying download pdb id again without bio unit (Fri Feb 9 06:36:25 2018)
  • completed download of PDB id 3o9p (size: 400 k, 5054 lines) (Fri Feb 9 06:36:25 2018)
  • converting pdb into xyzr (Fri Feb 9 06:36:25 2018)
  • completed conversion of PDB file: 3o9p-2018.feb09.841.pdb (size: 126k) (Fri Feb 9 06:36:28 2018)
  • converted 4046 atoms of 4046 atoms (Fri Feb 9 06:36:28 2018)
  • found 4046 atoms in pdb (Fri Feb 9 06:36:28 2018)
  • running 3v volume program (Fri Feb 9 06:36:28 2018)
  • smoothing out volume (Fri Feb 9 06:36:28 2018)
  • imaging volume (download mrc) with UCSF Chimera (Fri Feb 9 06:36:28 2018)
  • UCSF Chimera created Jmol compatible file (Fri Feb 9 06:36:37 2018)
  • compressing 3o9p-2018.feb09.841.obj (Fri Feb 9 06:36:37 2018)
  • UCSF Chimera completed in 8.83 sec (Fri Feb 9 06:36:37 2018)
  • analyzing volume (Fri Feb 9 06:36:37 2018)
  • normal CoM (-5.7, 1.4, 3.2) Å (Fri Feb 9 06:36:39 2018)
  • reduced center failed (Fri Feb 9 06:36:39 2018)
  • volume analysis completed in 2.21 sec (Fri Feb 9 06:36:39 2018)
  • compressing 3o9p-2018.feb09.841.mrc (Fri Feb 9 06:36:39 2018)
  • FINISHED (Fri Feb 9 06:36:39 2018)

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Log file display

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Terminal display
		
/var/www/html/output/2018/feb09/841 
Message: completed conversion of PDB file: 3o9p-2018.feb09.841.pdb (size: 126k) 
Message: converted 4046 atoms of 4046 atoms 
Message: found 4046 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2018/feb09/841/3o9p-2018.feb09.841.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 3o9p-2018.feb09.841.obj 
Message: UCSF Chimera completed in 8.83 sec 
OBJFILE /var/www/html/3vee/output/2018/feb09/841/3o9p-2018.feb09.841.obj.gz 
Message: analyzing volume 
Message: normal CoM (-5.7, 1.4, 3.2) Å 
Message: reduced center failed 
Message: volume analysis completed in 2.21 sec 
Message: compressing 3o9p-2018.feb09.841.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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