3v Running Log for JobId '2021.apr07.ff3'

Program is still running, progress is shown below

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  • host ip address=202.103.250.245 (Wed Apr 7 22:37:35 2021)
  • converting pdb into xyzr (Wed Apr 7 22:37:35 2021)
  • completed conversion of PDB file: 2021.apr07.ff3.pdb (size: 4k) (Wed Apr 7 22:37:36 2021)
  • converted 142 atoms of 142 atoms (Wed Apr 7 22:37:36 2021)
  • found 142 atoms in pdb (Wed Apr 7 22:37:36 2021)
  • starting probe size 0.000 (Wed Apr 7 22:37:36 2021)
  • running 3v volume program (Wed Apr 7 22:37:36 2021)
  • smoothing out volume (Wed Apr 7 22:37:36 2021)
  • imaging volume (download mrc) with UCSF Chimera (Wed Apr 7 22:37:36 2021)
  • UCSF Chimera created Jmol compatible file (Wed Apr 7 22:37:44 2021)
  • compressing 2021.apr07.ff3-0.0.obj (Wed Apr 7 22:37:44 2021)
  • UCSF Chimera completed in 8.18 sec (Wed Apr 7 22:37:44 2021)
  • analyzing volume (Wed Apr 7 22:37:44 2021)
  • normal CoM (4.7, -1.0, -5.5) Å (Wed Apr 7 22:37:44 2021)
  • reduced center failed (Wed Apr 7 22:37:44 2021)
  • volume analysis completed in 266.83 msec (Wed Apr 7 22:37:44 2021)
  • compressing 2021.apr07.ff3-0.0.mrc (Wed Apr 7 22:37:44 2021)
  • starting probe size 3.000 (Wed Apr 7 22:37:44 2021)
  • running 3v volume program (Wed Apr 7 22:37:44 2021)
  • smoothing out volume (Wed Apr 7 22:37:44 2021)
  • imaging volume (download mrc) with UCSF Chimera (Wed Apr 7 22:37:44 2021)
  • UCSF Chimera created Jmol compatible file (Wed Apr 7 22:37:52 2021)
  • compressing 2021.apr07.ff3-3.0.obj (Wed Apr 7 22:37:52 2021)
  • UCSF Chimera completed in 8.09 sec (Wed Apr 7 22:37:52 2021)
  • analyzing volume (Wed Apr 7 22:37:52 2021)
  • normal CoM (3.7, -1.0, -6.5) Å (Wed Apr 7 22:37:53 2021)
  • reduced center failed (Wed Apr 7 22:37:53 2021)
  • volume analysis completed in 0.61 sec (Wed Apr 7 22:37:53 2021)
  • compressing 2021.apr07.ff3-3.0.mrc (Wed Apr 7 22:37:53 2021)
  • starting probe size 6.000 (Wed Apr 7 22:37:53 2021)
  • running 3v volume program (Wed Apr 7 22:37:53 2021)
  • smoothing out volume (Wed Apr 7 22:37:53 2021)
  • imaging volume (download mrc) with UCSF Chimera (Wed Apr 7 22:37:53 2021)
  • UCSF Chimera created Jmol compatible file (Wed Apr 7 22:38:02 2021)
  • compressing 2021.apr07.ff3-6.0.obj (Wed Apr 7 22:38:02 2021)
  • UCSF Chimera completed in 9.16 sec (Wed Apr 7 22:38:03 2021)
  • analyzing volume (Wed Apr 7 22:38:03 2021)
  • normal CoM (4.7, -1.0, -5.5) Å (Wed Apr 7 22:38:03 2021)
  • reduced center failed (Wed Apr 7 22:38:04 2021)
  • volume analysis completed in 0.98 sec (Wed Apr 7 22:38:04 2021)
  • compressing 2021.apr07.ff3-6.0.mrc (Wed Apr 7 22:38:04 2021)
  • starting probe size 9.000 (Wed Apr 7 22:38:04 2021)
  • running 3v volume program (Wed Apr 7 22:38:04 2021)
  • smoothing out volume (Wed Apr 7 22:38:05 2021)
  • imaging volume (download mrc) with UCSF Chimera (Wed Apr 7 22:38:05 2021)
  • UCSF Chimera created Jmol compatible file (Wed Apr 7 22:38:13 2021)
  • compressing 2021.apr07.ff3-9.0.obj (Wed Apr 7 22:38:13 2021)
  • UCSF Chimera completed in 8.17 sec (Wed Apr 7 22:38:13 2021)
  • analyzing volume (Wed Apr 7 22:38:13 2021)
  • normal CoM (3.7, -1.0, -6.5) Å (Wed Apr 7 22:38:14 2021)
  • reduced center failed (Wed Apr 7 22:38:15 2021)
  • volume analysis completed in 1.65 sec (Wed Apr 7 22:38:15 2021)
  • compressing 2021.apr07.ff3-9.0.mrc (Wed Apr 7 22:38:15 2021)
  • tarring file list (Wed Apr 7 22:38:15 2021)
  • compressing 2021.apr07.ff3-0.0.mrc (Wed Apr 7 22:38:15 2021)
  • compressing 2021.apr07.ff3-3.0.mrc (Wed Apr 7 22:38:15 2021)
  • compressing 2021.apr07.ff3-6.0.mrc (Wed Apr 7 22:38:15 2021)
  • compressing 2021.apr07.ff3-9.0.mrc (Wed Apr 7 22:38:15 2021)
  • FINISHED (Wed Apr 7 22:38:15 2021)

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Log file display

Show last lines of log file 
Terminal display
		
wrote to mrc file: /var/www/html/3vee/output/2021/apr07/ff3/2021.apr07.ff3-9.0.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 2021.apr07.ff3-9.0.obj 
Message: UCSF Chimera completed in 8.17 sec 
OBJFILE /var/www/html/3vee/output/2021/apr07/ff3/2021.apr07.ff3-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (3.7, -1.0, -6.5) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.65 sec 
Message: compressing 2021.apr07.ff3-9.0.mrc 
Message: tarring file list 
Message: compressing 2021.apr07.ff3-0.0.mrc 
Message: compressing 2021.apr07.ff3-3.0.mrc 
Message: compressing 2021.apr07.ff3-6.0.mrc 
Message: compressing 2021.apr07.ff3-9.0.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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