3v Running Log for JobId '2017.oct12.efa'

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  • host ip address=134.76.70.252 (Thu Oct 12 09:28:20 2017)
  • converting pdb into xyzr (Thu Oct 12 09:28:21 2017)
  • completed conversion of PDB file: 2017.oct12.efa.pdb (size: 745k) (Thu Oct 12 09:28:29 2017)
  • converted 23852 atoms of 23852 atoms (Thu Oct 12 09:28:29 2017)
  • found 23852 atoms in pdb (Thu Oct 12 09:28:29 2017)
  • running 3v volume program (Thu Oct 12 09:28:29 2017)
  • smoothing out volume (Thu Oct 12 09:28:30 2017)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 12 09:28:31 2017)
  • UCSF Chimera created Jmol compatible file (Thu Oct 12 09:28:43 2017)
  • compressing 2017.oct12.efa.obj (Thu Oct 12 09:28:43 2017)
  • UCSF Chimera completed in 13.65 sec (Thu Oct 12 09:28:44 2017)
  • analyzing volume (Thu Oct 12 09:28:44 2017)
  • normal CoM (-2.6, -2.2, -1.1) Å (Thu Oct 12 09:28:48 2017)
  • reduced center failed (Thu Oct 12 09:28:48 2017)
  • volume analysis completed in 4.43 sec (Thu Oct 12 09:28:48 2017)
  • compressing 2017.oct12.efa.mrc (Thu Oct 12 09:28:48 2017)
  • FINISHED (Thu Oct 12 09:28:49 2017)

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Log file display

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Terminal display
		
/var/www/html/output/2017/oct12/efa 
Message: completed conversion of PDB file: 2017.oct12.efa.pdb (size: 745k) 
Message: converted 23852 atoms of 23852 atoms 
Message: found 23852 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2017/oct12/efa/2017.oct12.efa.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 2017.oct12.efa.obj 
Message: UCSF Chimera completed in 13.65 sec 
OBJFILE /var/www/html/3vee/output/2017/oct12/efa/2017.oct12.efa.obj.gz 
Message: analyzing volume 
Message: normal CoM (-2.6, -2.2, -1.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 4.43 sec 
Message: compressing 2017.oct12.efa.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] yahoo.com>
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