3v Running Log for JobId '2020.oct15.1b9'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=194.254.245.129 (Thu Oct 15 03:30:59 2020)
  • downloading pdb file (Thu Oct 15 03:30:59 2020)
  • failed to download pdb id: 4QKY (Thu Oct 15 03:30:59 2020)
  • trying download pdb id again without bio unit (Thu Oct 15 03:31:01 2020)
  • completed download of PDB id 4QKY (size: 634 k, 8012 lines) (Thu Oct 15 03:31:02 2020)
  • converting pdb into xyzr (Thu Oct 15 03:31:02 2020)
  • completed conversion of PDB file: 4QKY-2020.oct15.1b9.pdb (size: 116k) (Thu Oct 15 03:31:04 2020)
  • converted 3726 atoms of 3726 atoms (Thu Oct 15 03:31:04 2020)
  • found 3726 atoms in pdb (Thu Oct 15 03:31:04 2020)
  • starting probe size 0.000 (Thu Oct 15 03:31:04 2020)
  • running 3v volume program (Thu Oct 15 03:31:04 2020)
  • smoothing out volume (Thu Oct 15 03:31:05 2020)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 15 03:31:05 2020)
  • UCSF Chimera created Jmol compatible file (Thu Oct 15 03:31:10 2020)
  • compressing 4QKY-2020.oct15.1b9-0.0.obj (Thu Oct 15 03:31:10 2020)
  • UCSF Chimera completed in 5.29 sec (Thu Oct 15 03:31:10 2020)
  • analyzing volume (Thu Oct 15 03:31:10 2020)
  • normal CoM (-20.4, -0.4, 12.8) Å (Thu Oct 15 03:31:14 2020)
  • reduced center failed (Thu Oct 15 03:31:15 2020)
  • volume analysis completed in 4.71 sec (Thu Oct 15 03:31:15 2020)
  • compressing 4QKY-2020.oct15.1b9-0.0.mrc (Thu Oct 15 03:31:15 2020)
  • starting probe size 3.000 (Thu Oct 15 03:31:15 2020)
  • running 3v volume program (Thu Oct 15 03:31:15 2020)
  • smoothing out volume (Thu Oct 15 03:31:15 2020)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 15 03:31:15 2020)
  • UCSF Chimera created Jmol compatible file (Thu Oct 15 03:31:20 2020)
  • compressing 4QKY-2020.oct15.1b9-3.0.obj (Thu Oct 15 03:31:20 2020)
  • UCSF Chimera completed in 5.43 sec (Thu Oct 15 03:31:20 2020)
  • analyzing volume (Thu Oct 15 03:31:20 2020)
  • normal CoM (-16.7, -0.1, 8.9) Å (Thu Oct 15 03:31:26 2020)
  • reduced center failed (Thu Oct 15 03:31:26 2020)
  • volume analysis completed in 5.94 sec (Thu Oct 15 03:31:26 2020)
  • compressing 4QKY-2020.oct15.1b9-3.0.mrc (Thu Oct 15 03:31:26 2020)
  • starting probe size 6.000 (Thu Oct 15 03:31:27 2020)
  • running 3v volume program (Thu Oct 15 03:31:27 2020)
  • smoothing out volume (Thu Oct 15 03:31:27 2020)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 15 03:31:27 2020)
  • UCSF Chimera created Jmol compatible file (Thu Oct 15 03:31:32 2020)
  • compressing 4QKY-2020.oct15.1b9-6.0.obj (Thu Oct 15 03:31:32 2020)
  • UCSF Chimera completed in 5.38 sec (Thu Oct 15 03:31:32 2020)
  • analyzing volume (Thu Oct 15 03:31:32 2020)
  • normal CoM (-17.0, 0.2, 11.1) Å (Thu Oct 15 03:31:38 2020)
  • reduced center failed (Thu Oct 15 03:31:39 2020)
  • volume analysis completed in 6.43 sec (Thu Oct 15 03:31:39 2020)
  • compressing 4QKY-2020.oct15.1b9-6.0.mrc (Thu Oct 15 03:31:39 2020)
  • starting probe size 9.000 (Thu Oct 15 03:31:39 2020)
  • running 3v volume program (Thu Oct 15 03:31:39 2020)
  • smoothing out volume (Thu Oct 15 03:31:40 2020)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 15 03:31:40 2020)
  • UCSF Chimera created Jmol compatible file (Thu Oct 15 03:31:46 2020)
  • compressing 4QKY-2020.oct15.1b9-9.0.obj (Thu Oct 15 03:31:46 2020)
  • UCSF Chimera completed in 5.48 sec (Thu Oct 15 03:31:46 2020)
  • analyzing volume (Thu Oct 15 03:31:46 2020)
  • normal CoM (-21.1, 0.5, 13.0) Å (Thu Oct 15 03:31:52 2020)
  • reduced center failed (Thu Oct 15 03:31:54 2020)
  • volume analysis completed in 7.83 sec (Thu Oct 15 03:31:54 2020)
  • compressing 4QKY-2020.oct15.1b9-9.0.mrc (Thu Oct 15 03:31:54 2020)
  • tarring file list (Thu Oct 15 03:31:54 2020)
  • compressing 4QKY-2020.oct15.1b9-0.0.mrc (Thu Oct 15 03:31:54 2020)
  • compressing 4QKY-2020.oct15.1b9-3.0.mrc (Thu Oct 15 03:31:54 2020)
  • compressing 4QKY-2020.oct15.1b9-6.0.mrc (Thu Oct 15 03:31:54 2020)
  • compressing 4QKY-2020.oct15.1b9-9.0.mrc (Thu Oct 15 03:31:54 2020)
  • FINISHED (Thu Oct 15 03:31:54 2020)

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Log file display

Show last lines of log file 
Terminal display
		
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 4QKY-2020.oct15.1b9-9.0.obj 
Message: UCSF Chimera completed in 5.48 sec 
OBJFILE /var/www/html/3vee/output/2020/oct15/1b9/4QKY-2020.oct15.1b9-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-21.1, 0.5, 13.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 7.83 sec 
Message: compressing 4QKY-2020.oct15.1b9-9.0.mrc 
Message: tarring file list 
Message: compressing 4QKY-2020.oct15.1b9-0.0.mrc 
Message: compressing 4QKY-2020.oct15.1b9-3.0.mrc 
Message: compressing 4QKY-2020.oct15.1b9-6.0.mrc 
Me ... rundir: 
/var/www/html/3vee/output/2020/oct15/1b9 
COMPLETE SCRIPT:	55.11 sec 
ssage: compressing 4QKY-2020.oct15.1b9-9.0.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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