3v Running Log for JobId '2023.jan25.1bd'

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  • host ip address=202.3.77.208 (Wed Jan 25 08:58:49 2023)
  • converting pdb into xyzr (Wed Jan 25 08:58:49 2023)
  • completed conversion of PDB file: 2023.jan25.1bd.pdb (size: 269k) (Wed Jan 25 08:58:55 2023)
  • converted 8616 atoms of 8616 atoms (Wed Jan 25 08:58:55 2023)
  • found 8616 atoms in pdb (Wed Jan 25 08:58:55 2023)
  • running 3v volume program (Wed Jan 25 08:58:55 2023)
  • smoothing out volume (Wed Jan 25 08:58:56 2023)
  • imaging volume (download mrc) with UCSF Chimera (Wed Jan 25 08:58:56 2023)
  • UCSF Chimera created Jmol compatible file (Wed Jan 25 08:59:03 2023)
  • compressing 2023.jan25.1bd.obj (Wed Jan 25 08:59:03 2023)
  • UCSF Chimera completed in 7.38 sec (Wed Jan 25 08:59:03 2023)
  • analyzing volume (Wed Jan 25 08:59:03 2023)
  • normal CoM (21.6, 17.8, 11.2) Å (Wed Jan 25 08:59:17 2023)
  • reduced center failed (Wed Jan 25 08:59:19 2023)
  • volume analysis completed in 16.1 sec (Wed Jan 25 08:59:19 2023)
  • compressing 2023.jan25.1bd.mrc (Wed Jan 25 08:59:19 2023)
  • FINISHED (Wed Jan 25 08:59:20 2023)

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Log file display

Show last lines of log file  
Terminal display
		
/srv/output/2023/jan25/1bd 
Message: completed conversion of PDB file: 2023.jan25.1bd.pdb (size: 269k) 
Message: converted 8616 atoms of 8616 atoms 
Message: found 8616 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2023/jan25/1bd/2023.jan25.1bd.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 2023.jan25.1bd.obj 
Message: UCSF Chimera completed in 7.38 sec 
OBJFILE /var/www/html/3vee/output/2023/jan25/1bd/2023.jan25.1bd.obj.gz 
Message: analyzing volume 
Message: normal CoM (21.6, 17.8, 11.2) Å 
Message: reduced center failed 
Message: volume analysis completed in 16.1 sec 
Message: compressing 2023.jan25.1bd.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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