3v Running Log for JobId '2020.jun29.d31'

Program is still running, progress is shown below

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  • host ip address=137.97.17.253 (Mon Jun 29 12:42:23 2020)
  • downloading pdb file (Mon Jun 29 12:42:23 2020)
  • failed to download pdb id: 1qlp (Mon Jun 29 12:42:23 2020)
  • trying download pdb id again without bio unit (Mon Jun 29 12:42:25 2020)
  • completed download of PDB id 1qlp (size: 274 k, 3467 lines) (Mon Jun 29 12:42:25 2020)
  • converting pdb into xyzr (Mon Jun 29 12:42:25 2020)
  • completed conversion of PDB file: 1qlp-2020.jun29.d31.pdb (size: 92k) (Mon Jun 29 12:42:27 2020)
  • converted 2956 atoms of 2956 atoms (Mon Jun 29 12:42:27 2020)
  • found 2956 atoms in pdb (Mon Jun 29 12:42:27 2020)
  • running 3v volume program (Mon Jun 29 12:42:27 2020)
  • smoothing out volume (Mon Jun 29 12:42:28 2020)
  • imaging volume (download mrc) with UCSF Chimera (Mon Jun 29 12:42:28 2020)
  • UCSF Chimera created Jmol compatible file (Mon Jun 29 12:42:39 2020)
  • compressing 1qlp-2020.jun29.d31.obj (Mon Jun 29 12:42:39 2020)
  • UCSF Chimera completed in 13.12 sec (Mon Jun 29 12:42:41 2020)
  • analyzing volume (Mon Jun 29 12:42:41 2020)
  • normal CoM (-5.9, -1.9, 4.5) Å (Mon Jun 29 12:42:48 2020)
  • reduced center failed (Mon Jun 29 12:42:49 2020)
  • volume analysis completed in 8.4 sec (Mon Jun 29 12:42:49 2020)
  • compressing 1qlp-2020.jun29.d31.mrc (Mon Jun 29 12:42:49 2020)
  • FINISHED (Mon Jun 29 12:42:50 2020)

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Log file display

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Terminal display
		
/srv/output/2020/jun29/d31 
Message: completed conversion of PDB file: 1qlp-2020.jun29.d31.pdb (size: 92k) 
Message: converted 2956 atoms of 2956 atoms 
Message: found 2956 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2020/jun29/d31/1qlp-2020.jun29.d31.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 1qlp-2020.jun29.d31.obj 
Message: UCSF Chimera completed in 13.12 sec 
OBJFILE /var/www/html/3vee/output/2020/jun29/d31/1qlp-2020.jun29.d31.obj.gz 
Message: analyzing volume 
Message: normal CoM (-5.9, -1.9, 4.5) Å 
Message: reduced center failed 
Message: volume analysis completed in 8.4 sec 
Message: compressing 1qlp-2020.jun29.d31.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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