3v Running Log for JobId '2020.jul10.2ae'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=106.203.110.224 (Fri Jul 10 07:54:02 2020)
  • downloading pdb file (Fri Jul 10 07:54:02 2020)
  • failed to download pdb id: 1jj2 (Fri Jul 10 07:54:02 2020)
  • trying download pdb id again without bio unit (Fri Jul 10 07:54:04 2020)
  • completed download of PDB id 1jj2 (size: 8427 k, 106536 lines) (Fri Jul 10 07:54:05 2020)
  • converting pdb into xyzr (Fri Jul 10 07:54:05 2020)
  • completed conversion of PDB file: 1jj2-2020.jul10.2ae.pdb (size: 2826k) (Fri Jul 10 07:54:52 2020)
  • converted 90418 atoms of 90418 atoms (Fri Jul 10 07:54:52 2020)
  • found 90418 atoms in pdb (Fri Jul 10 07:54:52 2020)
  • running 3v exit tunnel program (Fri Jul 10 07:54:52 2020)
  • imaging volume (download mrc) with UCSF Chimera (Fri Jul 10 07:55:31 2020)
  • UCSF Chimera created Jmol compatible file (Fri Jul 10 07:56:08 2020)
  • compressing 1jj2-2020.jul10.2ae.obj (Fri Jul 10 07:56:08 2020)
  • UCSF Chimera completed in 37.57 sec (Fri Jul 10 07:56:08 2020)
  • analyzing volume (Fri Jul 10 07:56:08 2020)
  • normal CoM (-79.2, -105.0, -94.3) Å (Fri Jul 10 07:56:10 2020)
  • reduced center failed (Fri Jul 10 07:56:10 2020)
  • volume analysis completed in 1.26 sec (Fri Jul 10 07:56:10 2020)
  • compressing 1jj2-2020.jul10.2ae.mrc (Fri Jul 10 07:56:10 2020)
  • FINISHED (Fri Jul 10 07:56:10 2020)

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Log file display

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Terminal display
		
Message: converting pdb into xyzr 
/srv/output/2020/jul10/2ae 
Message: completed conversion of PDB file: 1jj2-2020.jul10.2ae.pdb (size: 2826k) 
Message: converted 90418 atoms of 90418 atoms 
Message: found 90418 atoms in pdb 
Message: running 3v exit tunnel program 
wrote to file: /var/www/html/3vee/output/2020/jul10/2ae/1jj2-2020.jul10.2ae.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 1jj2-2020.jul10.2ae.obj 
Message: UCSF Chimera completed in 37.57 sec 
OBJFILE /var/www/html/3vee/output/2020/jul10/2ae/1jj2-2020.jul10.2ae.obj.gz 
Message: analyzing volume 
Message: normal CoM (-79.2, -105.0, -94.3) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.26 sec 
Message: compressing 1jj2-2020.jul10.2ae.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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