3v Running Log for JobId '2017.mar18.90c'

Program is still running, progress is shown below

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  • host ip address=50.92.193.136 (Sat Mar 18 22:27:13 2017)
  • downloading pdb file (Sat Mar 18 22:27:13 2017)
  • completed download of PDB id 1dpx (size: 99 k, 1247 lines) (Sat Mar 18 22:27:13 2017)
  • converting pdb into xyzr (Sat Mar 18 22:27:13 2017)
  • completed conversion of PDB file: 1dpx-2017.mar18.90c.pdb (size: 32k) (Sat Mar 18 22:27:14 2017)
  • converted 1013 atoms of 1013 atoms (Sat Mar 18 22:27:14 2017)
  • found 1013 atoms in pdb (Sat Mar 18 22:27:14 2017)
  • running 3v volume program (Sat Mar 18 22:27:14 2017)
  • smoothing out volume (Sat Mar 18 22:27:14 2017)
  • imaging volume (download mrc) with UCSF Chimera (Sat Mar 18 22:27:14 2017)
  • UCSF Chimera created Jmol compatible file (Sat Mar 18 22:27:21 2017)
  • compressing 1dpx-2017.mar18.90c.obj (Sat Mar 18 22:27:21 2017)
  • UCSF Chimera completed in 6.97 sec (Sat Mar 18 22:27:21 2017)
  • analyzing volume (Sat Mar 18 22:27:21 2017)
  • normal CoM (-4.6, -4.5, 0.6) Å (Sat Mar 18 22:27:22 2017)
  • reduced center failed (Sat Mar 18 22:27:22 2017)
  • volume analysis completed in 0.76 sec (Sat Mar 18 22:27:22 2017)
  • compressing 1dpx-2017.mar18.90c.mrc (Sat Mar 18 22:27:22 2017)
  • FINISHED (Sat Mar 18 22:27:22 2017)

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Log file display

Show last lines of log file 
Terminal display
		
/var/www/html/output/2017/mar18/90c 
Message: completed conversion of PDB file: 1dpx-2017.mar18.90c.pdb (size: 32k) 
Message: converted 1013 atoms of 1013 atoms 
Message: found 1013 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2017/mar18/90c/1dpx-2017.mar18.90c.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 1dpx-2017.mar18.90c.obj 
Message: UCSF Chimera completed in 6.97 sec 
OBJFILE /var/www/html/3vee/output/2017/mar18/90c/1dpx-2017.mar18.90c.obj.gz 
Message: analyzing volume 
Message: normal CoM (-4.6, -4.5, 0.6) Å 
Message: reduced center failed 
Message: volume analysis completed in 0.76 sec 
Message: compressing 1dpx-2017.mar18.90c.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] yahoo.com>
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