3v Running Log for JobId '2023.jan24.9bf'

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  • host ip address=134.21.217.164 (Tue Jan 24 10:54:58 2023)
  • converting pdb into xyzr (Tue Jan 24 10:54:58 2023)
  • completed conversion of PDB file: 2023.jan24.9bf.pdb (size: 13k) (Tue Jan 24 10:54:58 2023)
  • converted 411 atoms of 411 atoms (Tue Jan 24 10:54:58 2023)
  • found 411 atoms in pdb (Tue Jan 24 10:54:58 2023)
  • running 3v volume program (Tue Jan 24 10:54:58 2023)
  • smoothing out volume (Tue Jan 24 10:54:58 2023)
  • imaging volume (download mrc) with UCSF Chimera (Tue Jan 24 10:54:58 2023)
  • UCSF Chimera created Jmol compatible file (Tue Jan 24 10:55:05 2023)
  • compressing 2023.jan24.9bf.obj (Tue Jan 24 10:55:05 2023)
  • UCSF Chimera completed in 7.07 sec (Tue Jan 24 10:55:05 2023)
  • analyzing volume (Tue Jan 24 10:55:05 2023)
  • normal CoM (-8.8, -2.7, 2.9) Å (Tue Jan 24 10:55:06 2023)
  • reduced center failed (Tue Jan 24 10:55:06 2023)
  • volume analysis completed in 346.99 msec (Tue Jan 24 10:55:06 2023)
  • compressing 2023.jan24.9bf.mrc (Tue Jan 24 10:55:06 2023)
  • FINISHED (Tue Jan 24 10:55:06 2023)

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Log file display

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Terminal display
		
/srv/output/2023/jan24/9bf 
Message: completed conversion of PDB file: 2023.jan24.9bf.pdb (size: 13k) 
Message: converted 411 atoms of 411 atoms 
Message: found 411 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2023/jan24/9bf/2023.jan24.9bf.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.jan24.9bf.obj 
Message: UCSF Chimera completed in 7.07 sec 
OBJFILE /var/www/html/3vee/output/2023/jan24/9bf/2023.jan24.9bf.obj.gz 
Message: analyzing volume 
Message: normal CoM (-8.8, -2.7, 2.9) Å 
Message: reduced center failed 
Message: volume analysis completed in 346.99 msec 
Message: compressing 2023.jan24.9bf.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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