3v Running Log for JobId '2019.jun27.c3d'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=195.178.200.86 (Thu Jun 27 05:28:04 2019)
  • converting pdb into xyzr (Thu Jun 27 05:28:04 2019)
  • completed conversion of PDB file: 2019.jun27.c3d.pdb (size: 137k) (Thu Jun 27 05:28:07 2019)
  • converted 4370 atoms of 4370 atoms (Thu Jun 27 05:28:07 2019)
  • found 4370 atoms in pdb (Thu Jun 27 05:28:07 2019)
  • starting probe size 0.000 (Thu Jun 27 05:28:07 2019)
  • running 3v volume program (Thu Jun 27 05:28:07 2019)
  • smoothing out volume (Thu Jun 27 05:28:08 2019)
  • imaging volume (download mrc) with UCSF Chimera (Thu Jun 27 05:28:08 2019)
  • UCSF Chimera created Jmol compatible file (Thu Jun 27 05:28:29 2019)
  • compressing 2019.jun27.c3d-0.0.obj (Thu Jun 27 05:28:29 2019)
  • UCSF Chimera completed in 23.37 sec (Thu Jun 27 05:28:32 2019)
  • analyzing volume (Thu Jun 27 05:28:32 2019)
  • normal CoM (-3.9, -0.9, 2.5) Å (Thu Jun 27 05:28:41 2019)
  • reduced center failed (Thu Jun 27 05:28:42 2019)
  • volume analysis completed in 10.35 sec (Thu Jun 27 05:28:42 2019)
  • compressing 2019.jun27.c3d-0.0.pdb (Thu Jun 27 05:28:42 2019)
  • compressing 2019.jun27.c3d-0.0.mrc (Thu Jun 27 05:28:46 2019)
  • starting probe size 1.400 (Thu Jun 27 05:28:48 2019)
  • running 3v volume program (Thu Jun 27 05:28:48 2019)
  • smoothing out volume (Thu Jun 27 05:28:49 2019)
  • imaging volume (download mrc) with UCSF Chimera (Thu Jun 27 05:28:50 2019)
  • UCSF Chimera created Jmol compatible file (Thu Jun 27 05:29:05 2019)
  • compressing 2019.jun27.c3d-1.4.obj (Thu Jun 27 05:29:05 2019)
  • UCSF Chimera completed in 17.11 sec (Thu Jun 27 05:29:07 2019)
  • analyzing volume (Thu Jun 27 05:29:07 2019)
  • normal CoM (-3.9, -1.9, 2.5) Å (Thu Jun 27 05:29:18 2019)
  • reduced center failed (Thu Jun 27 05:29:20 2019)
  • volume analysis completed in 13.26 sec (Thu Jun 27 05:29:20 2019)
  • compressing 2019.jun27.c3d-1.4.pdb (Thu Jun 27 05:29:20 2019)
  • compressing 2019.jun27.c3d-1.4.mrc (Thu Jun 27 05:29:22 2019)
  • tarring file list (Thu Jun 27 05:29:23 2019)
  • compressing 2019.jun27.c3d-0.0.pdb (Thu Jun 27 05:29:23 2019)
  • compressing 2019.jun27.c3d-0.0.mrc (Thu Jun 27 05:29:23 2019)
  • compressing 2019.jun27.c3d-1.4.pdb (Thu Jun 27 05:29:23 2019)
  • compressing 2019.jun27.c3d-1.4.mrc (Thu Jun 27 05:29:23 2019)
  • FINISHED (Thu Jun 27 05:29:23 2019)

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Log file display

Show last lines of log file 
Terminal display
		
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 2019.jun27.c3d-1.4.obj 
Message: UCSF Chimera completed in 17.11 sec 
OBJFILE /var/www/html/3vee/output/2019/jun27/c3d/2019.jun27.c3d-1.4.obj.gz 
Message: analyzing volume 
Message: normal CoM (-3.9, -1.9, 2.5) Å 
Message: reduced center failed 
Message: volume analysis completed in 13.26 sec 
Message: compressing 2019.jun27.c3d-1.4.pdb 
Message: compressing 2019.jun27.c3d-1.4.mrc 
Message: tarring file list 
Message: compressing 2019.jun27.c3d-0.0.pdb 
Message: compressing 2019.jun27.c3d-0.0.mrc 
Message: compressing 2019.jun27.c3d-1.4.pdb 
Message: compressing 2019.jun27.c3d-1.4.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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