3v Running Log for JobId '2020.aug01.bd0'

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  • host ip address=106.84.13.223 (Sat Aug 1 09:57:32 2020)
  • converting pdb into xyzr (Sat Aug 1 09:57:33 2020)
  • completed conversion of PDB file: 2020.aug01.bd0.pdb (size: 5k) (Sat Aug 1 09:57:33 2020)
  • converted 149 atoms of 149 atoms (Sat Aug 1 09:57:33 2020)
  • found 149 atoms in pdb (Sat Aug 1 09:57:33 2020)
  • running 3v volume program (Sat Aug 1 09:57:33 2020)
  • smoothing out volume (Sat Aug 1 09:57:33 2020)
  • imaging volume (download mrc) with UCSF Chimera (Sat Aug 1 09:57:33 2020)
  • UCSF Chimera created Jmol compatible file (Sat Aug 1 09:57:39 2020)
  • compressing 2020.aug01.bd0.obj (Sat Aug 1 09:57:39 2020)
  • UCSF Chimera completed in 6.29 sec (Sat Aug 1 09:57:39 2020)
  • analyzing volume (Sat Aug 1 09:57:39 2020)
  • normal CoM (-1.4, 0.2, -3.4) Å (Sat Aug 1 09:57:39 2020)
  • reduced center failed (Sat Aug 1 09:57:39 2020)
  • volume analysis completed in 171.4 msec (Sat Aug 1 09:57:39 2020)
  • compressing 2020.aug01.bd0.mrc (Sat Aug 1 09:57:39 2020)
  • FINISHED (Sat Aug 1 09:57:39 2020)

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Log file display

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Terminal display
		
/srv/output/2020/aug01/bd0 
Message: completed conversion of PDB file: 2020.aug01.bd0.pdb (size: 5k) 
Message: converted 149 atoms of 149 atoms 
Message: found 149 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2020/aug01/bd0/2020.aug01.bd0.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 2020.aug01.bd0.obj 
Message: UCSF Chimera completed in 6.29 sec 
OBJFILE /var/www/html/3vee/output/2020/aug01/bd0/2020.aug01.bd0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-1.4, 0.2, -3.4) Å 
Message: reduced center failed 
Message: volume analysis completed in 171.4 msec 
Message: compressing 2020.aug01.bd0.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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