3v Running Log for JobId '2019.oct07.923'

Program is still running, progress is shown below

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  • host ip address=193.147.148.112 (Mon Oct 7 06:28:53 2019)
  • converting pdb into xyzr (Mon Oct 7 06:28:53 2019)
  • completed conversion of PDB file: 2019.oct07.923.pdb (size: 845k) (Mon Oct 7 06:29:04 2019)
  • converted 27055 atoms of 27055 atoms (Mon Oct 7 06:29:04 2019)
  • found 27055 atoms in pdb (Mon Oct 7 06:29:04 2019)
  • running 3v solvent program (Mon Oct 7 06:29:04 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Oct 7 06:29:10 2019)
  • UCSF Chimera created Jmol compatible file (Mon Oct 7 06:29:26 2019)
  • compressing 2019.oct07.923.obj (Mon Oct 7 06:29:26 2019)
  • UCSF Chimera completed in 18.41 sec (Mon Oct 7 06:29:28 2019)
  • analyzing volume (Mon Oct 7 06:29:28 2019)
  • normal CoM (-4.6, -18.4, -4.3) Å (Mon Oct 7 06:29:35 2019)
  • reduced center failed (Mon Oct 7 06:29:36 2019)
  • volume analysis completed in 7.89 sec (Mon Oct 7 06:29:36 2019)
  • compressing 2019.oct07.923.mrc (Mon Oct 7 06:29:36 2019)
  • FINISHED (Mon Oct 7 06:29:37 2019)

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Log file display

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Terminal display
		
Message: converting pdb into xyzr 
/srv/output/2019/oct07/923 
Message: completed conversion of PDB file: 2019.oct07.923.pdb (size: 845k) 
Message: converted 27055 atoms of 27055 atoms 
Message: found 27055 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2019/oct07/923/2019.oct07.923.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2019.oct07.923.obj 
Message: UCSF Chimera completed in 18.41 sec 
OBJFILE /var/www/html/3vee/output/2019/oct07/923/2019.oct07.923.obj.gz 
Message: analyzing volume 
Message: normal CoM (-4.6, -18.4, -4.3) Å 
Message: reduced center failed 
Message: volume analysis completed in 7.89 sec 
Message: compressing 2019.oct07.923.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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