3v Running Log for JobId '2023.jan23.6d2'

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  • host ip address=132.183.4.6 (Mon Jan 23 19:28:49 2023)
  • converting pdb into xyzr (Mon Jan 23 19:28:49 2023)
  • completed conversion of PDB file: 2023.jan23.6d2.pdb (size: 110k) (Mon Jan 23 19:28:52 2023)
  • converted 3518 atoms of 3518 atoms (Mon Jan 23 19:28:52 2023)
  • found 3518 atoms in pdb (Mon Jan 23 19:28:52 2023)
  • running 3v solvent program (Mon Jan 23 19:28:52 2023)
  • imaging volume (download mrc) with UCSF Chimera (Mon Jan 23 19:30:02 2023)
  • UCSF Chimera created Jmol compatible file (Mon Jan 23 19:30:55 2023)
  • compressing 2023.jan23.6d2.obj (Mon Jan 23 19:30:55 2023)
  • UCSF Chimera completed in 63.08 sec (Mon Jan 23 19:31:05 2023)
  • analyzing volume (Mon Jan 23 19:31:05 2023)
  • normal CoM (-54.7, -4.0, -10.7) Å (Mon Jan 23 19:32:24 2023)
  • reduced center failed (Mon Jan 23 19:32:44 2023)
  • volume analysis completed in 1 min 39 sec (Mon Jan 23 19:32:44 2023)
  • compressing 2023.jan23.6d2.pdb (Mon Jan 23 19:32:44 2023)
  • compressing 2023.jan23.6d2.mrc (Mon Jan 23 19:32:46 2023)
  • FINISHED (Mon Jan 23 19:32:51 2023)

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Log file display

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Terminal display
		
/srv/output/2023/jan23/6d2 
Message: completed conversion of PDB file: 2023.jan23.6d2.pdb (size: 110k) 
Message: converted 3518 atoms of 3518 atoms 
Message: found 3518 atoms in pdb 
Message: running 3v solvent program 
wrote to file: /var/www/html/3vee/output/2023/jan23/6d2/2023.jan23.6d2.mrc 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2023.jan23.6d2.obj 
Message: UCSF Chimera completed in 63.08 sec 
OBJFILE /var/www/html/3vee/output/2023/jan23/6d2/2023.jan23.6d2.obj.gz 
Message: analyzing volume 
Message: normal CoM (-54.7, -4.0, -10.7) Å 
Message: reduced center failed 
Message: volume analysis completed in 1 min 39 sec 
Message: compressing 2023.jan23.6d2.pdb 
Message: compressing 2023.jan23.6d2.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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