3v Running Log for JobId '2017.oct11.cff'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=123.24.184.55 (Thu Oct 12 00:36:14 2017)
  • converting pdb into xyzr (Thu Oct 12 00:36:14 2017)
  • completed conversion of PDB file: 2017.oct11.cff.pdb (size: 73k) (Thu Oct 12 00:36:16 2017)
  • converted 2331 atoms of 2331 atoms (Thu Oct 12 00:36:16 2017)
  • found 2331 atoms in pdb (Thu Oct 12 00:36:16 2017)
  • starting probe size 0.000 (Thu Oct 12 00:36:16 2017)
  • running 3v volume program (Thu Oct 12 00:36:16 2017)
  • smoothing out volume (Thu Oct 12 00:36:16 2017)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 12 00:36:16 2017)
  • UCSF Chimera created Jmol compatible file (Thu Oct 12 00:36:25 2017)
  • compressing 2017.oct11.cff-0.0.obj (Thu Oct 12 00:36:25 2017)
  • UCSF Chimera completed in 9.11 sec (Thu Oct 12 00:36:25 2017)
  • analyzing volume (Thu Oct 12 00:36:25 2017)
  • normal CoM (-2.7, -2.2, -3.8) Å (Thu Oct 12 00:36:26 2017)
  • reduced center failed (Thu Oct 12 00:36:26 2017)
  • volume analysis completed in 0.91 sec (Thu Oct 12 00:36:26 2017)
  • compressing 2017.oct11.cff-0.0.mrc (Thu Oct 12 00:36:26 2017)
  • starting probe size 3.000 (Thu Oct 12 00:36:26 2017)
  • running 3v volume program (Thu Oct 12 00:36:26 2017)
  • smoothing out volume (Thu Oct 12 00:36:26 2017)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 12 00:36:26 2017)
  • UCSF Chimera created Jmol compatible file (Thu Oct 12 00:36:36 2017)
  • compressing 2017.oct11.cff-3.0.obj (Thu Oct 12 00:36:36 2017)
  • UCSF Chimera completed in 10.14 sec (Thu Oct 12 00:36:36 2017)
  • analyzing volume (Thu Oct 12 00:36:36 2017)
  • normal CoM (-2.8, -0.3, -3.8) Å (Thu Oct 12 00:36:38 2017)
  • reduced center failed (Thu Oct 12 00:36:38 2017)
  • volume analysis completed in 1.33 sec (Thu Oct 12 00:36:38 2017)
  • compressing 2017.oct11.cff-3.0.mrc (Thu Oct 12 00:36:38 2017)
  • starting probe size 6.000 (Thu Oct 12 00:36:38 2017)
  • running 3v volume program (Thu Oct 12 00:36:38 2017)
  • smoothing out volume (Thu Oct 12 00:36:38 2017)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 12 00:36:38 2017)
  • UCSF Chimera created Jmol compatible file (Thu Oct 12 00:36:47 2017)
  • compressing 2017.oct11.cff-6.0.obj (Thu Oct 12 00:36:47 2017)
  • UCSF Chimera completed in 9.24 sec (Thu Oct 12 00:36:47 2017)
  • analyzing volume (Thu Oct 12 00:36:47 2017)
  • normal CoM (-0.9, -2.2, -7.8) Å (Thu Oct 12 00:36:49 2017)
  • reduced center failed (Thu Oct 12 00:36:49 2017)
  • volume analysis completed in 1.64 sec (Thu Oct 12 00:36:49 2017)
  • compressing 2017.oct11.cff-6.0.mrc (Thu Oct 12 00:36:49 2017)
  • starting probe size 9.000 (Thu Oct 12 00:36:49 2017)
  • running 3v volume program (Thu Oct 12 00:36:49 2017)
  • smoothing out volume (Thu Oct 12 00:36:50 2017)
  • imaging volume (download mrc) with UCSF Chimera (Thu Oct 12 00:36:50 2017)
  • UCSF Chimera created Jmol compatible file (Thu Oct 12 00:36:59 2017)
  • compressing 2017.oct11.cff-9.0.obj (Thu Oct 12 00:36:59 2017)
  • UCSF Chimera completed in 9.6 sec (Thu Oct 12 00:36:59 2017)
  • analyzing volume (Thu Oct 12 00:36:59 2017)
  • normal CoM (-4.9, -2.2, -3.7) Å (Thu Oct 12 00:37:01 2017)
  • reduced center failed (Thu Oct 12 00:37:01 2017)
  • volume analysis completed in 1.95 sec (Thu Oct 12 00:37:01 2017)
  • compressing 2017.oct11.cff-9.0.mrc (Thu Oct 12 00:37:01 2017)
  • tarring file list (Thu Oct 12 00:37:01 2017)
  • compressing 2017.oct11.cff-0.0.mrc (Thu Oct 12 00:37:01 2017)
  • compressing 2017.oct11.cff-3.0.mrc (Thu Oct 12 00:37:01 2017)
  • compressing 2017.oct11.cff-6.0.mrc (Thu Oct 12 00:37:01 2017)
  • compressing 2017.oct11.cff-9.0.mrc (Thu Oct 12 00:37:01 2017)
  • FINISHED (Thu Oct 12 00:37:01 2017)

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Log file display

Show last lines of log file 
Terminal display
		
wrote to mrc file: /var/www/html/3vee/output/2017/oct11/cff/2017.oct11.cff-9.0.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 2017.oct11.cff-9.0.obj 
Message: UCSF Chimera completed in 9.6 sec 
OBJFILE /var/www/html/3vee/output/2017/oct11/cff/2017.oct11.cff-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-4.9, -2.2, -3.7) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.95 sec 
Message: compressing 2017.oct11.cff-9.0.mrc 
Message: tarring file list 
Message: compressing 2017.oct11.cff-0.0.mrc 
Message: compressing 2017.oct11.cff-3.0.mrc 
Message: compressing 2017.oct11.cff-6.0.mrc 
Message: compressing 2017.oct11.cff-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] yahoo.com>
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