3v Running Log for JobId '2023.may25.be3'

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  • host ip address=138.23.11.177 (Thu May 25 13:20:50 2023)
  • converting pdb into xyzr (Thu May 25 13:20:50 2023)
  • completed conversion of PDB file: 2023.may25.be3.pdb (size: 3k) (Thu May 25 13:20:50 2023)
  • converted 111 atoms of 111 atoms (Thu May 25 13:20:50 2023)
  • found 111 atoms in pdb (Thu May 25 13:20:50 2023)
  • running 3v volume program (Thu May 25 13:20:50 2023)
  • smoothing out volume (Thu May 25 13:20:50 2023)
  • imaging volume (download mrc) with UCSF Chimera (Thu May 25 13:20:51 2023)
  • UCSF Chimera created Jmol compatible file (Thu May 25 13:20:57 2023)
  • compressing 2023.may25.be3.obj (Thu May 25 13:20:57 2023)
  • UCSF Chimera completed in 6.98 sec (Thu May 25 13:20:57 2023)
  • analyzing volume (Thu May 25 13:20:57 2023)
  • normal CoM (-0.9, -3.2, -1.1) Å (Thu May 25 13:20:58 2023)
  • reduced center failed (Thu May 25 13:20:58 2023)
  • volume analysis completed in 124.33 msec (Thu May 25 13:20:58 2023)
  • compressing 2023.may25.be3.mrc (Thu May 25 13:20:58 2023)
  • FINISHED (Thu May 25 13:20:58 2023)

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Log file display

Show last lines of log file  
Terminal display
		
/srv/output/2023/may25/be3 
Message: completed conversion of PDB file: 2023.may25.be3.pdb (size: 3k) 
Message: converted 111 atoms of 111 atoms 
Message: found 111 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2023/may25/be3/2023.may25.be3.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.may25.be3.obj 
Message: UCSF Chimera completed in 6.98 sec 
OBJFILE /var/www/html/3vee/output/2023/may25/be3/2023.may25.be3.obj.gz 
Message: analyzing volume 
Message: normal CoM (-0.9, -3.2, -1.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 124.33 msec 
Message: compressing 2023.may25.be3.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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