3v Running Log for JobId '2021.feb20.8d9'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=117.181.48.125 (Sun Feb 21 00:29:28 2021)
  • converting pdb into xyzr (Sun Feb 21 00:29:28 2021)
  • completed conversion of PDB file: 2021.feb20.8d9.pdb (size: 5k) (Sun Feb 21 00:29:28 2021)
  • converted 147 atoms of 147 atoms (Sun Feb 21 00:29:28 2021)
  • found 147 atoms in pdb (Sun Feb 21 00:29:28 2021)
  • starting probe size 0.000 (Sun Feb 21 00:29:28 2021)
  • running 3v volume program (Sun Feb 21 00:29:28 2021)
  • smoothing out volume (Sun Feb 21 00:29:28 2021)
  • imaging volume (download mrc) with UCSF Chimera (Sun Feb 21 00:29:28 2021)
  • UCSF Chimera created Jmol compatible file (Sun Feb 21 00:29:33 2021)
  • compressing 2021.feb20.8d9-0.0.obj (Sun Feb 21 00:29:33 2021)
  • UCSF Chimera completed in 4.78 sec (Sun Feb 21 00:29:33 2021)
  • analyzing volume (Sun Feb 21 00:29:33 2021)
  • normal CoM (-5.2, -4.3, 4.5) Å (Sun Feb 21 00:29:33 2021)
  • reduced center failed (Sun Feb 21 00:29:33 2021)
  • volume analysis completed in 414.53 msec (Sun Feb 21 00:29:33 2021)
  • compressing 2021.feb20.8d9-0.0.mrc (Sun Feb 21 00:29:33 2021)
  • starting probe size 3.000 (Sun Feb 21 00:29:33 2021)
  • running 3v volume program (Sun Feb 21 00:29:33 2021)
  • smoothing out volume (Sun Feb 21 00:29:33 2021)
  • imaging volume (download mrc) with UCSF Chimera (Sun Feb 21 00:29:33 2021)
  • UCSF Chimera created Jmol compatible file (Sun Feb 21 00:29:39 2021)
  • compressing 2021.feb20.8d9-3.0.obj (Sun Feb 21 00:29:39 2021)
  • UCSF Chimera completed in 5.53 sec (Sun Feb 21 00:29:39 2021)
  • analyzing volume (Sun Feb 21 00:29:39 2021)
  • normal CoM (-3.2, -4.8, 3.9) Å (Sun Feb 21 00:29:39 2021)
  • reduced center failed (Sun Feb 21 00:29:40 2021)
  • volume analysis completed in 0.75 sec (Sun Feb 21 00:29:40 2021)
  • compressing 2021.feb20.8d9-3.0.mrc (Sun Feb 21 00:29:40 2021)
  • starting probe size 6.000 (Sun Feb 21 00:29:40 2021)
  • running 3v volume program (Sun Feb 21 00:29:40 2021)
  • smoothing out volume (Sun Feb 21 00:29:40 2021)
  • imaging volume (download mrc) with UCSF Chimera (Sun Feb 21 00:29:40 2021)
  • UCSF Chimera created Jmol compatible file (Sun Feb 21 00:29:46 2021)
  • compressing 2021.feb20.8d9-6.0.obj (Sun Feb 21 00:29:46 2021)
  • UCSF Chimera completed in 6.21 sec (Sun Feb 21 00:29:46 2021)
  • analyzing volume (Sun Feb 21 00:29:46 2021)
  • normal CoM (-5.2, -2.1, 3.3) Å (Sun Feb 21 00:29:48 2021)
  • reduced center failed (Sun Feb 21 00:29:48 2021)
  • volume analysis completed in 1.37 sec (Sun Feb 21 00:29:48 2021)
  • compressing 2021.feb20.8d9-6.0.mrc (Sun Feb 21 00:29:48 2021)
  • starting probe size 9.000 (Sun Feb 21 00:29:48 2021)
  • running 3v volume program (Sun Feb 21 00:29:48 2021)
  • smoothing out volume (Sun Feb 21 00:29:49 2021)
  • imaging volume (download mrc) with UCSF Chimera (Sun Feb 21 00:29:49 2021)
  • UCSF Chimera created Jmol compatible file (Sun Feb 21 00:29:56 2021)
  • compressing 2021.feb20.8d9-9.0.obj (Sun Feb 21 00:29:56 2021)
  • UCSF Chimera completed in 6.44 sec (Sun Feb 21 00:29:56 2021)
  • analyzing volume (Sun Feb 21 00:29:56 2021)
  • normal CoM (-3.2, -1.7, 2.0) Å (Sun Feb 21 00:29:58 2021)
  • reduced center failed (Sun Feb 21 00:29:58 2021)
  • volume analysis completed in 1.98 sec (Sun Feb 21 00:29:58 2021)
  • compressing 2021.feb20.8d9-9.0.mrc (Sun Feb 21 00:29:58 2021)
  • tarring file list (Sun Feb 21 00:29:58 2021)
  • compressing 2021.feb20.8d9-0.0.mrc (Sun Feb 21 00:29:58 2021)
  • compressing 2021.feb20.8d9-3.0.mrc (Sun Feb 21 00:29:58 2021)
  • compressing 2021.feb20.8d9-6.0.mrc (Sun Feb 21 00:29:58 2021)
  • compressing 2021.feb20.8d9-9.0.mrc (Sun Feb 21 00:29:58 2021)
  • FINISHED (Sun Feb 21 00:29:58 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/feb20/8d9/2021.feb20.8d9-9.0.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.feb20.8d9-9.0.obj 
Message: UCSF Chimera completed in 6.44 sec 
OBJFILE /var/www/html/3vee/output/2021/feb20/8d9/2021.feb20.8d9-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-3.2, -1.7, 2.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 1.98 sec 
Message: compressing 2021.feb20.8d9-9.0.mrc 
Message: tarring file list 
Message: compressing 2021.feb20.8d9-0.0.mrc 
Message: compressing 2021.feb20.8d9-3.0.mrc 
Message: compressing 2021.feb20.8d9-6.0.mrc 
Message: compressing 2021.feb20.8d9-9.0.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
Download source code
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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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