3v Running Log for JobId '2019.apr12.414'

Program is still running, progress is shown below

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  • host ip address=128.252.116.102 (Fri Apr 12 16:12:48 2019)
  • downloading pdb file (Fri Apr 12 16:12:48 2019)
  • failed to download pdb id: 1sjr (Fri Apr 12 16:12:48 2019)
  • trying download pdb id again without bio unit (Fri Apr 12 16:12:51 2019)
  • completed download of PDB id 1sjr (size: 2227 k, 28150 lines) (Fri Apr 12 16:12:51 2019)
  • converting pdb into xyzr (Fri Apr 12 16:12:51 2019)
  • completed conversion of PDB file: 1sjr-2019.apr12.414.pdb (size: 864k) (Fri Apr 12 16:13:01 2019)
  • converted 27632 atoms of 27632 atoms (Fri Apr 12 16:13:01 2019)
  • found 27632 atoms in pdb (Fri Apr 12 16:13:01 2019)
  • running 3v volume program (Fri Apr 12 16:13:01 2019)
  • smoothing out volume (Fri Apr 12 16:13:02 2019)
  • imaging volume (download mrc) with UCSF Chimera (Fri Apr 12 16:13:02 2019)
  • UCSF Chimera created Jmol compatible file (Fri Apr 12 16:13:09 2019)
  • compressing 1sjr-2019.apr12.414.obj (Fri Apr 12 16:13:09 2019)
  • UCSF Chimera completed in 7.13 sec (Fri Apr 12 16:13:09 2019)
  • analyzing volume (Fri Apr 12 16:13:09 2019)
  • normal CoM (-4.7, -0.6, -4.3) Å (Fri Apr 12 16:13:10 2019)
  • reduced center failed (Fri Apr 12 16:13:10 2019)
  • volume analysis completed in 1.09 sec (Fri Apr 12 16:13:10 2019)
  • compressing 1sjr-2019.apr12.414.mrc (Fri Apr 12 16:13:10 2019)
  • FINISHED (Fri Apr 12 16:13:10 2019)

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Log file display

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Terminal display
		
/srv/output/2019/apr12/414 
Message: completed conversion of PDB file: 1sjr-2019.apr12.414.pdb (size: 864k) 
Message: converted 27632 atoms of 27632 atoms 
Message: found 27632 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/apr12/414/1sjr-2019.apr12.414.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 1sjr-2019.apr12.414.obj 
Message: UCSF Chimera completed in 7.13 sec 
OBJFILE /var/www/html/3vee/output/2019/apr12/414/1sjr-2019.apr12.414.obj.gz 
Message: analyzing volume 
Message: normal CoM (-4.7, -0.6, -4.3) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.09 sec 
Message: compressing 1sjr-2019.apr12.414.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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