3v Running Log for JobId '2022.jun23.0c2'

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  • host ip address=222.97.221.63 (Thu Jun 23 12:27:52 2022)
  • downloading pdb file (Thu Jun 23 12:27:52 2022)
  • completed download of PDB id 1k53 (size: 58 k, 728 lines) (Thu Jun 23 12:27:53 2022)
  • converting pdb into xyzr (Thu Jun 23 12:27:53 2022)
  • completed conversion of PDB file: 1k53-2022.jun23.0c2.pdb (size: 18k) (Thu Jun 23 12:27:53 2022)
  • converted 569 atoms of 569 atoms (Thu Jun 23 12:27:53 2022)
  • found 569 atoms in pdb (Thu Jun 23 12:27:53 2022)
  • running 3v volume program (Thu Jun 23 12:27:53 2022)
  • smoothing out volume (Thu Jun 23 12:27:53 2022)
  • imaging volume (download mrc) with UCSF Chimera (Thu Jun 23 12:27:53 2022)
  • UCSF Chimera created Jmol compatible file (Thu Jun 23 12:28:00 2022)
  • compressing 1k53-2022.jun23.0c2.obj (Thu Jun 23 12:28:00 2022)
  • UCSF Chimera completed in 6.79 sec (Thu Jun 23 12:28:00 2022)
  • analyzing volume (Thu Jun 23 12:28:00 2022)
  • normal CoM (-4.2, 1.9, -0.8) Å (Thu Jun 23 12:28:00 2022)
  • reduced center failed (Thu Jun 23 12:28:01 2022)
  • volume analysis completed in 0.59 sec (Thu Jun 23 12:28:01 2022)
  • compressing 1k53-2022.jun23.0c2.mrc (Thu Jun 23 12:28:01 2022)
  • FINISHED (Thu Jun 23 12:28:01 2022)

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Log file display

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Terminal display
		
/srv/output/2022/jun23/0c2 
Message: completed conversion of PDB file: 1k53-2022.jun23.0c2.pdb (size: 18k) 
Message: converted 569 atoms of 569 atoms 
Message: found 569 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2022/jun23/0c2/1k53-2022.jun23.0c2.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 1k53-2022.jun23.0c2.obj 
Message: UCSF Chimera completed in 6.79 sec 
OBJFILE /var/www/html/3vee/output/2022/jun23/0c2/1k53-2022.jun23.0c2.obj.gz 
Message: analyzing volume 
Message: normal CoM (-4.2, 1.9, -0.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 0.59 sec 
Message: compressing 1k53-2022.jun23.0c2.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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