3v Running Log for JobId '2022.may13.014'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=157.0.207.64 (Fri May 13 10:56:33 2022)
  • converting pdb into xyzr (Fri May 13 10:56:33 2022)
  • completed conversion of PDB file: 2022.may13.014.pdb (size: 16k) (Fri May 13 10:56:33 2022)
  • converted 496 atoms of 496 atoms (Fri May 13 10:56:33 2022)
  • found 496 atoms in pdb (Fri May 13 10:56:33 2022)
  • starting probe size 0.000 (Fri May 13 10:56:33 2022)
  • running 3v volume program (Fri May 13 10:56:33 2022)
  • smoothing out volume (Fri May 13 10:56:33 2022)
  • imaging volume (download mrc) with UCSF Chimera (Fri May 13 10:56:34 2022)
  • UCSF Chimera created Jmol compatible file (Fri May 13 10:56:40 2022)
  • compressing 2022.may13.014-0.0.obj (Fri May 13 10:56:40 2022)
  • UCSF Chimera completed in 6.25 sec (Fri May 13 10:56:40 2022)
  • analyzing volume (Fri May 13 10:56:40 2022)
  • normal CoM (1.1, -4.7, -1.9) Å (Fri May 13 10:56:40 2022)
  • reduced center failed (Fri May 13 10:56:40 2022)
  • volume analysis completed in 298.41 msec (Fri May 13 10:56:40 2022)
  • compressing 2022.may13.014-0.0.mrc (Fri May 13 10:56:40 2022)
  • starting probe size 3.000 (Fri May 13 10:56:40 2022)
  • running 3v volume program (Fri May 13 10:56:40 2022)
  • smoothing out volume (Fri May 13 10:56:40 2022)
  • imaging volume (download mrc) with UCSF Chimera (Fri May 13 10:56:40 2022)
  • UCSF Chimera created Jmol compatible file (Fri May 13 10:56:46 2022)
  • compressing 2022.may13.014-3.0.obj (Fri May 13 10:56:46 2022)
  • UCSF Chimera completed in 5.93 sec (Fri May 13 10:56:46 2022)
  • analyzing volume (Fri May 13 10:56:46 2022)
  • normal CoM (3.1, -4.7, -5.8) Å (Fri May 13 10:56:47 2022)
  • reduced center failed (Fri May 13 10:56:47 2022)
  • volume analysis completed in 445.29 msec (Fri May 13 10:56:47 2022)
  • compressing 2022.may13.014-3.0.mrc (Fri May 13 10:56:47 2022)
  • starting probe size 6.000 (Fri May 13 10:56:47 2022)
  • running 3v volume program (Fri May 13 10:56:47 2022)
  • smoothing out volume (Fri May 13 10:56:47 2022)
  • imaging volume (download mrc) with UCSF Chimera (Fri May 13 10:56:47 2022)
  • UCSF Chimera created Jmol compatible file (Fri May 13 10:56:54 2022)
  • compressing 2022.may13.014-6.0.obj (Fri May 13 10:56:54 2022)
  • UCSF Chimera completed in 7.08 sec (Fri May 13 10:56:54 2022)
  • analyzing volume (Fri May 13 10:56:54 2022)
  • normal CoM (5.1, -2.7, -5.9) Å (Fri May 13 10:56:54 2022)
  • reduced center failed (Fri May 13 10:56:54 2022)
  • volume analysis completed in 0.6 sec (Fri May 13 10:56:54 2022)
  • compressing 2022.may13.014-6.0.mrc (Fri May 13 10:56:54 2022)
  • starting probe size 9.000 (Fri May 13 10:56:54 2022)
  • running 3v volume program (Fri May 13 10:56:54 2022)
  • smoothing out volume (Fri May 13 10:56:55 2022)
  • imaging volume (download mrc) with UCSF Chimera (Fri May 13 10:56:55 2022)
  • UCSF Chimera created Jmol compatible file (Fri May 13 10:57:01 2022)
  • compressing 2022.may13.014-9.0.obj (Fri May 13 10:57:01 2022)
  • UCSF Chimera completed in 6.77 sec (Fri May 13 10:57:01 2022)
  • analyzing volume (Fri May 13 10:57:01 2022)
  • normal CoM (1.1, -4.7, -1.9) Å (Fri May 13 10:57:02 2022)
  • reduced center failed (Fri May 13 10:57:02 2022)
  • volume analysis completed in 0.74 sec (Fri May 13 10:57:02 2022)
  • compressing 2022.may13.014-9.0.mrc (Fri May 13 10:57:02 2022)
  • tarring file list (Fri May 13 10:57:02 2022)
  • compressing 2022.may13.014-0.0.mrc (Fri May 13 10:57:02 2022)
  • compressing 2022.may13.014-3.0.mrc (Fri May 13 10:57:02 2022)
  • compressing 2022.may13.014-6.0.mrc (Fri May 13 10:57:02 2022)
  • compressing 2022.may13.014-9.0.mrc (Fri May 13 10:57:02 2022)
  • FINISHED (Fri May 13 10:57:02 2022)

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Log file display

Show last lines of log file  
Terminal display
		
wrote to mrc file: /var/www/html/3vee/output/2022/may13/014/2022.may13.014-9.0.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 2022.may13.014-9.0.obj 
Message: UCSF Chimera completed in 6.77 sec 
OBJFILE /var/www/html/3vee/output/2022/may13/014/2022.may13.014-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (1.1, -4.7, -1.9) Å 
Message: reduced center failed 
Message: volume analysis completed in 0.74 sec 
Message: compressing 2022.may13.014-9.0.mrc 
Message: tarring file list 
Message: compressing 2022.may13.014-0.0.mrc 
Message: compressing 2022.may13.014-3.0.mrc 
Message: compressing 2022.may13.014-6.0.mrc 
Message: compressing 2022.may13.014-9.0.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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