3v Running Log for JobId '2019.aug09.163'

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  • host ip address=113.106.172.152 (Fri Aug 9 18:46:33 2019)
  • converting pdb into xyzr (Fri Aug 9 18:46:33 2019)
  • completed conversion of PDB file: 2019.aug09.163.pdb (size: 188k) (Fri Aug 9 18:46:37 2019)
  • converted 6015 atoms of 6015 atoms (Fri Aug 9 18:46:37 2019)
  • found 6015 atoms in pdb (Fri Aug 9 18:46:37 2019)
  • running 3v volume program (Fri Aug 9 18:46:37 2019)
  • smoothing out volume (Fri Aug 9 18:46:38 2019)
  • imaging volume (download mrc) with UCSF Chimera (Fri Aug 9 18:46:38 2019)
  • UCSF Chimera created Jmol compatible file (Fri Aug 9 18:46:49 2019)
  • compressing 2019.aug09.163.obj (Fri Aug 9 18:46:49 2019)
  • UCSF Chimera completed in 11.7 sec (Fri Aug 9 18:46:49 2019)
  • analyzing volume (Fri Aug 9 18:46:49 2019)
  • normal CoM (1.9, -3.7, -2.4) Å (Fri Aug 9 18:46:52 2019)
  • reduced center failed (Fri Aug 9 18:46:53 2019)
  • volume analysis completed in 3.24 sec (Fri Aug 9 18:46:53 2019)
  • compressing 2019.aug09.163.mrc (Fri Aug 9 18:46:53 2019)
  • FINISHED (Fri Aug 9 18:46:53 2019)

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Log file display

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Terminal display
		
/srv/output/2019/aug09/163 
Message: completed conversion of PDB file: 2019.aug09.163.pdb (size: 188k) 
Message: converted 6015 atoms of 6015 atoms 
Message: found 6015 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/aug09/163/2019.aug09.163.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.aug09.163.obj 
Message: UCSF Chimera completed in 11.7 sec 
OBJFILE /var/www/html/3vee/output/2019/aug09/163/2019.aug09.163.obj.gz 
Message: analyzing volume 
Message: normal CoM (1.9, -3.7, -2.4) Å 
Message: reduced center failed 
Message: volume analysis completed in 3.24 sec 
Message: compressing 2019.aug09.163.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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