3v Running Log for JobId '2020.oct16.34f'

Program is still running, progress is shown below

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  • host ip address=71.231.179.102 (Sat Oct 17 01:58:03 2020)
  • downloading pdb file (Sat Oct 17 01:58:03 2020)
  • failed to download pdb id: 1hzh (Sat Oct 17 01:58:03 2020)
  • trying download pdb id again without bio unit (Sat Oct 17 01:58:05 2020)
  • completed download of PDB id 1hzh (size: 928 k, 11728 lines) (Sat Oct 17 01:58:06 2020)
  • converting pdb into xyzr (Sat Oct 17 01:58:06 2020)
  • completed conversion of PDB file: 1hzh-2020.oct16.34f.pdb (size: 324k) (Sat Oct 17 01:58:13 2020)
  • converted 10355 atoms of 10355 atoms (Sat Oct 17 01:58:13 2020)
  • found 10355 atoms in pdb (Sat Oct 17 01:58:13 2020)
  • running 3v volume program (Sat Oct 17 01:58:13 2020)
  • smoothing out volume (Sat Oct 17 01:58:14 2020)
  • imaging volume (download mrc) with UCSF Chimera (Sat Oct 17 01:58:14 2020)
  • UCSF Chimera created Jmol compatible file (Sat Oct 17 01:58:22 2020)
  • compressing 1hzh-2020.oct16.34f.obj (Sat Oct 17 01:58:22 2020)
  • UCSF Chimera completed in 8.68 sec (Sat Oct 17 01:58:23 2020)
  • analyzing volume (Sat Oct 17 01:58:23 2020)
  • normal CoM (15.2, 3.8, -17.3) Å (Sat Oct 17 01:58:33 2020)
  • reduced center failed (Sat Oct 17 01:58:35 2020)
  • volume analysis completed in 12.48 sec (Sat Oct 17 01:58:35 2020)
  • compressing 1hzh-2020.oct16.34f.mrc (Sat Oct 17 01:58:35 2020)
  • FINISHED (Sat Oct 17 01:58:36 2020)

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Log file display

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Terminal display
		
/srv/output/2020/oct16/34f 
Message: completed conversion of PDB file: 1hzh-2020.oct16.34f.pdb (size: 324k) 
Message: converted 10355 atoms of 10355 atoms 
Message: found 10355 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2020/oct16/34f/1hzh-2020.oct16.34f.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 1hzh-2020.oct16.34f.obj 
Message: UCSF Chimera completed in 8.68 sec 
OBJFILE /var/www/html/3vee/output/2020/oct16/34f/1hzh-2020.oct16.34f.obj.gz 
Message: analyzing volume 
Message: normal CoM (15.2, 3.8, -17.3) Å 
Message: reduced center failed 
Message: volume analysis completed in 12.48 sec 
Message: compressing 1hzh-2020.oct16.34f.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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