3v Running Log for JobId '2023.jan24.335'

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  • host ip address=128.119.146.130 (Tue Jan 24 10:23:55 2023)
  • converting pdb into xyzr (Tue Jan 24 10:23:55 2023)
  • completed conversion of PDB file: 2023.jan24.335.pdb (size: 0k) (Tue Jan 24 10:23:55 2023)
  • converted 9 atoms of 9 atoms (Tue Jan 24 10:23:55 2023)
  • found 9 atoms in pdb (Tue Jan 24 10:23:55 2023)
  • running 3v volume program (Tue Jan 24 10:23:55 2023)
  • smoothing out volume (Tue Jan 24 10:23:55 2023)
  • imaging volume (download mrc) with UCSF Chimera (Tue Jan 24 10:23:56 2023)
  • UCSF Chimera created Jmol compatible file (Tue Jan 24 10:23:57 2023)
  • compressing 2023.jan24.335.obj (Tue Jan 24 10:23:57 2023)
  • UCSF Chimera completed in 1.91 sec (Tue Jan 24 10:23:57 2023)
  • analyzing volume (Tue Jan 24 10:23:57 2023)
  • normal CoM (-1.2, -1.8, -0.2) Å (Tue Jan 24 10:23:58 2023)
  • volume analysis completed in 127.67 msec (Tue Jan 24 10:23:58 2023)
  • compressing 2023.jan24.335.mrc (Tue Jan 24 10:23:58 2023)
  • FINISHED (Tue Jan 24 10:23:58 2023)

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Log file display

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Terminal display
		
Message: converting pdb into xyzr 
/srv/output/2023/jan24/335 
Message: completed conversion of PDB file: 2023.jan24.335.pdb (size: 0k) 
Message: converted 9 atoms of 9 atoms 
Message: found 9 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2023/jan24/335/2023.jan24.335.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.jan24.335.obj 
Message: UCSF Chimera completed in 1.91 sec 
OBJFILE /var/www/html/3vee/output/2023/jan24/335/2023.jan24.335.obj.gz 
Message: analyzing volume 
Message: normal CoM (-1.2, -1.8, -0.2) Å 
Message: volume analysis completed in 127.67 msec 
Message: compressing 2023.jan24.335.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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