3v Running Log for JobId '2019.aug29.a7b'

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  • host ip address=147.251.40.215 (Thu Aug 29 06:31:51 2019)
  • converting pdb into xyzr (Thu Aug 29 06:31:51 2019)
  • completed conversion of PDB file: 2019.aug29.a7b.pdb (size: 76k) (Thu Aug 29 06:31:53 2019)
  • converted 2425 atoms of 2425 atoms (Thu Aug 29 06:31:53 2019)
  • found 2425 atoms in pdb (Thu Aug 29 06:31:53 2019)
  • running 3v solvent program (Thu Aug 29 06:31:53 2019)
  • imaging volume (download mrc) with UCSF Chimera (Thu Aug 29 06:31:55 2019)
  • UCSF Chimera created Jmol compatible file (Thu Aug 29 06:31:57 2019)
  • compressing 2019.aug29.a7b.obj (Thu Aug 29 06:31:57 2019)
  • UCSF Chimera completed in 2.27 sec (Thu Aug 29 06:31:57 2019)
  • analyzing volume (Thu Aug 29 06:31:57 2019)
  • normal CoM (-19.0, 1.3, -8.2) Å (Thu Aug 29 06:32:00 2019)
  • reduced center failed (Thu Aug 29 06:32:01 2019)
  • volume analysis completed in 3.57 sec (Thu Aug 29 06:32:01 2019)
  • compressing 2019.aug29.a7b.pdb (Thu Aug 29 06:32:01 2019)
  • compressing 2019.aug29.a7b.mrc (Thu Aug 29 06:32:01 2019)
  • FINISHED (Thu Aug 29 06:32:01 2019)

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Log file display

Show last lines of log file 
Terminal display
		
/srv/output/2019/aug29/a7b 
Message: completed conversion of PDB file: 2019.aug29.a7b.pdb (size: 76k) 
Message: converted 2425 atoms of 2425 atoms 
Message: found 2425 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2019/aug29/a7b/2019.aug29.a7b.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2019.aug29.a7b.obj 
Message: UCSF Chimera completed in 2.27 sec 
OBJFILE /var/www/html/3vee/output/2019/aug29/a7b/2019.aug29.a7b.obj.gz 
Message: analyzing volume 
Message: normal CoM (-19.0, 1.3, -8.2) Å 
Message: reduced center failed 
Message: volume analysis completed in 3.57 sec 
Message: compressing 2019.aug29.a7b.pdb 
Message: compressing 2019.aug29.a7b.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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