3v Running Log for JobId '2017.aug11.4a0'

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  • host ip address=117.201.233.16 (Sat Aug 12 00:07:44 2017)
  • converting pdb into xyzr (Sat Aug 12 00:07:44 2017)
  • completed conversion of PDB file: 2017.aug11.4a0.pdb (size: 6723k) (Sat Aug 12 00:09:00 2017)
  • converted 215130 atoms of 215130 atoms (Sat Aug 12 00:09:00 2017)
  • found 215130 atoms in pdb (Sat Aug 12 00:09:00 2017)
  • running 3v volume program (Sat Aug 12 00:09:00 2017)
  • smoothing out volume (Sat Aug 12 00:09:16 2017)
  • imaging volume (download mrc) with UCSF Chimera (Sat Aug 12 00:09:24 2017)
  • UCSF Chimera created Jmol compatible file (Sat Aug 12 00:10:56 2017)
  • compressing 2017.aug11.4a0.obj (Sat Aug 12 00:10:56 2017)
  • UCSF Chimera completed in 2 min 19 sec (Sat Aug 12 00:11:35 2017)
  • analyzing volume (Sat Aug 12 00:11:35 2017)
  • normal CoM (-98.5, -0.4, 96.2) Å (Sat Aug 12 00:17:40 2017)
  • reduced center failed (Sat Aug 12 00:19:21 2017)
  • volume analysis completed in 7 min 46 sec (Sat Aug 12 00:19:21 2017)
  • compressing 2017.aug11.4a0.mrc (Sat Aug 12 00:19:21 2017)
  • FINISHED (Sat Aug 12 00:19:40 2017)

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Log file display

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Terminal display
		
/var/www/html/output/2017/aug11/4a0 
Message: completed conversion of PDB file: 2017.aug11.4a0.pdb (size: 6723k) 
Message: converted 215130 atoms of 215130 atoms 
Message: found 215130 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2017/aug11/4a0/2017.aug11.4a0.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.aug11.4a0.obj 
Message: UCSF Chimera completed in 2 min 19 sec 
OBJFILE /var/www/html/3vee/output/2017/aug11/4a0/2017.aug11.4a0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-98.5, -0.4, 96.2) Å 
Message: reduced center failed 
Message: volume analysis completed in 7 min 46 sec 
Message: compressing 2017.aug11.4a0.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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