3v Running Log for JobId '2023.jan24.d83'

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  • host ip address=134.21.217.164 (Tue Jan 24 07:48:37 2023)
  • converting pdb into xyzr (Tue Jan 24 07:48:37 2023)
  • completed conversion of PDB file: 2023.jan24.d83.pdb (size: 137k) (Tue Jan 24 07:48:40 2023)
  • converted 4385 atoms of 4385 atoms (Tue Jan 24 07:48:40 2023)
  • found 4385 atoms in pdb (Tue Jan 24 07:48:40 2023)
  • running 3v volume program (Tue Jan 24 07:48:40 2023)
  • smoothing out volume (Tue Jan 24 07:48:41 2023)
  • imaging volume (download mrc) with UCSF Chimera (Tue Jan 24 07:48:41 2023)
  • UCSF Chimera created Jmol compatible file (Tue Jan 24 07:48:49 2023)
  • compressing 2023.jan24.d83.obj (Tue Jan 24 07:48:49 2023)
  • UCSF Chimera completed in 8.6 sec (Tue Jan 24 07:48:49 2023)
  • analyzing volume (Tue Jan 24 07:48:49 2023)
  • normal CoM (-5.0, -1.4, 4.4) Å (Tue Jan 24 07:48:52 2023)
  • reduced center failed (Tue Jan 24 07:48:52 2023)
  • volume analysis completed in 3.3 sec (Tue Jan 24 07:48:52 2023)
  • compressing 2023.jan24.d83.mrc (Tue Jan 24 07:48:52 2023)
  • FINISHED (Tue Jan 24 07:48:53 2023)

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Log file display

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Terminal display
		
/srv/output/2023/jan24/d83 
Message: completed conversion of PDB file: 2023.jan24.d83.pdb (size: 137k) 
Message: converted 4385 atoms of 4385 atoms 
Message: found 4385 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2023/jan24/d83/2023.jan24.d83.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 2023.jan24.d83.obj 
Message: UCSF Chimera completed in 8.6 sec 
OBJFILE /var/www/html/3vee/output/2023/jan24/d83/2023.jan24.d83.obj.gz 
Message: analyzing volume 
Message: normal CoM (-5.0, -1.4, 4.4) Å 
Message: reduced center failed 
Message: volume analysis completed in 3.3 sec 
Message: compressing 2023.jan24.d83.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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