3v Running Log for JobId '2019.aug11.c2e'

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  • host ip address=73.76.17.247 (Sun Aug 11 11:21:29 2019)
  • downloading pdb file (Sun Aug 11 11:21:29 2019)
  • failed to download pdb id: 4ls9 (Sun Aug 11 11:21:29 2019)
  • trying download pdb id again without bio unit (Sun Aug 11 11:21:31 2019)
  • completed download of PDB id 4ls9 (size: 841 k, 10636 lines) (Sun Aug 11 11:21:31 2019)
  • converting pdb into xyzr (Sun Aug 11 11:21:31 2019)
  • completed conversion of PDB file: 4ls9-2019.aug11.c2e.pdb (size: 147k) (Sun Aug 11 11:21:35 2019)
  • converted 4699 atoms of 4699 atoms (Sun Aug 11 11:21:35 2019)
  • found 4699 atoms in pdb (Sun Aug 11 11:21:35 2019)
  • running 3v volume program (Sun Aug 11 11:21:35 2019)
  • smoothing out volume (Sun Aug 11 11:21:35 2019)
  • imaging volume (download mrc) with UCSF Chimera (Sun Aug 11 11:21:35 2019)
  • UCSF Chimera created Jmol compatible file (Sun Aug 11 11:21:44 2019)
  • compressing 4ls9-2019.aug11.c2e.obj (Sun Aug 11 11:21:44 2019)
  • UCSF Chimera completed in 9.05 sec (Sun Aug 11 11:21:44 2019)
  • analyzing volume (Sun Aug 11 11:21:44 2019)
  • normal CoM (-2.8, -4.3, 0.6) Å (Sun Aug 11 11:21:46 2019)
  • reduced center failed (Sun Aug 11 11:21:47 2019)
  • volume analysis completed in 3.05 sec (Sun Aug 11 11:21:47 2019)
  • compressing 4ls9-2019.aug11.c2e.mrc (Sun Aug 11 11:21:47 2019)
  • FINISHED (Sun Aug 11 11:21:47 2019)

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Log file display

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Terminal display
		
/srv/output/2019/aug11/c2e 
Message: completed conversion of PDB file: 4ls9-2019.aug11.c2e.pdb (size: 147k) 
Message: converted 4699 atoms of 4699 atoms 
Message: found 4699 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/aug11/c2e/4ls9-2019.aug11.c2e.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 4ls9-2019.aug11.c2e.obj 
Message: UCSF Chimera completed in 9.05 sec 
OBJFILE /var/www/html/3vee/output/2019/aug11/c2e/4ls9-2019.aug11.c2e.obj.gz 
Message: analyzing volume 
Message: normal CoM (-2.8, -4.3, 0.6) Å 
Message: reduced center failed 
Message: volume analysis completed in 3.05 sec 
Message: compressing 4ls9-2019.aug11.c2e.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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