3v Running Log for JobId '2020.sep15.cbd'

Program is still running, progress is shown below

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  • host ip address=195.54.210.131 (Tue Sep 15 05:58:28 2020)
  • waiting for system load (18.33) to calm down, total wait time: 1 hr 27 min (Tue Sep 15 05:58:29 2020)
  • running now (Tue Sep 15 07:25:14 2020)
  • downloading pdb file (Tue Sep 15 07:25:14 2020)
  • failed to download pdb id: 4PQE (Tue Sep 15 07:25:14 2020)
  • trying download pdb id again without bio unit (Tue Sep 15 07:25:16 2020)
  • completed download of PDB id 4PQE (size: 365 k, 4611 lines) (Tue Sep 15 07:25:17 2020)
  • converting pdb into xyzr (Tue Sep 15 07:25:17 2020)
  • completed conversion of PDB file: 4PQE-2020.sep15.cbd.pdb (size: 128k) (Tue Sep 15 07:25:20 2020)
  • converted 4087 atoms of 4087 atoms (Tue Sep 15 07:25:20 2020)
  • found 4087 atoms in pdb (Tue Sep 15 07:25:20 2020)
  • running 3v volume program (Tue Sep 15 07:25:20 2020)
  • smoothing out volume (Tue Sep 15 07:25:20 2020)
  • imaging volume (download mrc) with UCSF Chimera (Tue Sep 15 07:25:20 2020)
  • UCSF Chimera created Jmol compatible file (Tue Sep 15 07:25:30 2020)
  • compressing 4PQE-2020.sep15.cbd.obj (Tue Sep 15 07:25:30 2020)
  • UCSF Chimera completed in 9.76 sec (Tue Sep 15 07:25:30 2020)
  • analyzing volume (Tue Sep 15 07:25:30 2020)
  • normal CoM (-5.4, -3.6, 0.7) Å (Tue Sep 15 07:25:32 2020)
  • reduced center failed (Tue Sep 15 07:25:32 2020)
  • volume analysis completed in 2.22 sec (Tue Sep 15 07:25:32 2020)
  • compressing 4PQE-2020.sep15.cbd.mrc (Tue Sep 15 07:25:32 2020)
  • FINISHED (Tue Sep 15 07:25:32 2020)

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Log file display

Show last lines of log file 
Terminal display
		
/srv/output/2020/sep15/cbd 
Message: completed conversion of PDB file: 4PQE-2020.sep15.cbd.pdb (size: 128k) 
Message: converted 4087 atoms of 4087 atoms 
Message: found 4087 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2020/sep15/cbd/4PQE-2020.sep15.cbd.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 4PQE-2020.sep15.cbd.obj 
Message: UCSF Chimera completed in 9.76 sec 
OBJFILE /var/www/html/3vee/output/2020/sep15/cbd/4PQE-2020.sep15.cbd.obj.gz 
Message: analyzing volume 
Message: normal CoM (-5.4, -3.6, 0.7) Å 
Message: reduced center failed 
Message: volume analysis completed in 2.22 sec 
Message: compressing 4PQE-2020.sep15.cbd.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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