3v Running Log for JobId '2019.aug09.e57'

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  • host ip address=129.171.249.144 (Fri Aug 9 16:35:31 2019)
  • converting pdb into xyzr (Fri Aug 9 16:35:31 2019)
  • completed conversion of PDB file: 2019.aug09.e57.pdb (size: 12k) (Fri Aug 9 16:35:32 2019)
  • converted 368 atoms of 368 atoms (Fri Aug 9 16:35:32 2019)
  • found 368 atoms in pdb (Fri Aug 9 16:35:32 2019)
  • running 3v volume program (Fri Aug 9 16:35:32 2019)
  • smoothing out volume (Fri Aug 9 16:35:32 2019)
  • imaging volume (download mrc) with UCSF Chimera (Fri Aug 9 16:35:32 2019)
  • UCSF Chimera created Jmol compatible file (Fri Aug 9 16:35:42 2019)
  • compressing 2019.aug09.e57.obj (Fri Aug 9 16:35:42 2019)
  • UCSF Chimera completed in 10.26 sec (Fri Aug 9 16:35:42 2019)
  • analyzing volume (Fri Aug 9 16:35:42 2019)
  • normal CoM (6.8, 0.2, -5.8) Å (Fri Aug 9 16:35:43 2019)
  • reduced center failed (Fri Aug 9 16:35:44 2019)
  • volume analysis completed in 1.46 sec (Fri Aug 9 16:35:44 2019)
  • compressing 2019.aug09.e57.pdb (Fri Aug 9 16:35:44 2019)
  • compressing 2019.aug09.e57.mrc (Fri Aug 9 16:35:44 2019)
  • FINISHED (Fri Aug 9 16:35:44 2019)

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Log file display

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Terminal display
		
Message: completed conversion of PDB file: 2019.aug09.e57.pdb (size: 12k) 
Message: converted 368 atoms of 368 atoms 
Message: found 368 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/aug09/e57/2019.aug09.e57.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 2019.aug09.e57.obj 
Message: UCSF Chimera completed in 10.26 sec 
OBJFILE /var/www/html/3vee/output/2019/aug09/e57/2019.aug09.e57.obj.gz 
Message: analyzing volume 
Message: normal CoM (6.8, 0.2, -5.8) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.46 sec 
Message: compressing 2019.aug09.e57.pdb 
Message: compressing 2019.aug09.e57.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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