3v Running Log for JobId '2020.mar24.a7d'

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  • host ip address=95.90.243.92 (Tue Mar 24 18:34:58 2020)
  • converting pdb into xyzr (Tue Mar 24 18:34:58 2020)
  • completed conversion of PDB file: 2020.mar24.a7d.pdb (size: 414k) (Tue Mar 24 18:35:09 2020)
  • converted 13246 atoms of 13246 atoms (Tue Mar 24 18:35:09 2020)
  • found 13246 atoms in pdb (Tue Mar 24 18:35:09 2020)
  • running 3v volume program (Tue Mar 24 18:35:09 2020)
  • smoothing out volume (Tue Mar 24 18:35:09 2020)
  • imaging volume (download mrc) with UCSF Chimera (Tue Mar 24 18:35:09 2020)
  • UCSF Chimera created Jmol compatible file (Tue Mar 24 18:35:19 2020)
  • compressing 2020.mar24.a7d.obj (Tue Mar 24 18:35:19 2020)
  • UCSF Chimera completed in 10.4 sec (Tue Mar 24 18:35:19 2020)
  • analyzing volume (Tue Mar 24 18:35:19 2020)
  • normal CoM (25.4, -1.5, -31.2) Å (Tue Mar 24 18:35:26 2020)
  • reduced center failed (Tue Mar 24 18:35:28 2020)
  • volume analysis completed in 8.11 sec (Tue Mar 24 18:35:28 2020)
  • compressing 2020.mar24.a7d.mrc (Tue Mar 24 18:35:28 2020)
  • FINISHED (Tue Mar 24 18:35:28 2020)

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Log file display

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Terminal display
		
/srv/output/2020/mar24/a7d 
Message: completed conversion of PDB file: 2020.mar24.a7d.pdb (size: 414k) 
Message: converted 13246 atoms of 13246 atoms 
Message: found 13246 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2020/mar24/a7d/2020.mar24.a7d.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.mar24.a7d.obj 
Message: UCSF Chimera completed in 10.4 sec 
OBJFILE /var/www/html/3vee/output/2020/mar24/a7d/2020.mar24.a7d.obj.gz 
Message: analyzing volume 
Message: normal CoM (25.4, -1.5, -31.2) Å 
Message: reduced center failed 
Message: volume analysis completed in 8.11 sec 
Message: compressing 2020.mar24.a7d.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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