3v Running Log for JobId '2023.jan22.5cd'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=111.91.225.18 (Sun Jan 22 09:02:12 2023)
  • converting pdb into xyzr (Sun Jan 22 09:02:12 2023)
  • completed conversion of PDB file: 2023.jan22.5cd.pdb (size: 69k) (Sun Jan 22 09:02:13 2023)
  • converted 2220 atoms of 2220 atoms (Sun Jan 22 09:02:13 2023)
  • found 2220 atoms in pdb (Sun Jan 22 09:02:13 2023)
  • starting probe size 0.000 (Sun Jan 22 09:02:13 2023)
  • running 3v volume program (Sun Jan 22 09:02:13 2023)
  • smoothing out volume (Sun Jan 22 09:02:13 2023)
  • imaging volume (download mrc) with UCSF Chimera (Sun Jan 22 09:02:13 2023)
  • UCSF Chimera created Jmol compatible file (Sun Jan 22 09:02:23 2023)
  • compressing 2023.jan22.5cd-0.0.obj (Sun Jan 22 09:02:23 2023)
  • UCSF Chimera completed in 10.03 sec (Sun Jan 22 09:02:23 2023)
  • analyzing volume (Sun Jan 22 09:02:23 2023)
  • normal CoM (-1.0, 0.3, 3.5) Å (Sun Jan 22 09:02:24 2023)
  • reduced center failed (Sun Jan 22 09:02:24 2023)
  • volume analysis completed in 1.02 sec (Sun Jan 22 09:02:24 2023)
  • compressing 2023.jan22.5cd-0.0.mrc (Sun Jan 22 09:02:24 2023)
  • starting probe size 3.000 (Sun Jan 22 09:02:25 2023)
  • running 3v volume program (Sun Jan 22 09:02:25 2023)
  • smoothing out volume (Sun Jan 22 09:02:25 2023)
  • imaging volume (download mrc) with UCSF Chimera (Sun Jan 22 09:02:25 2023)
  • UCSF Chimera created Jmol compatible file (Sun Jan 22 09:02:35 2023)
  • compressing 2023.jan22.5cd-3.0.obj (Sun Jan 22 09:02:35 2023)
  • UCSF Chimera completed in 9.88 sec (Sun Jan 22 09:02:35 2023)
  • analyzing volume (Sun Jan 22 09:02:35 2023)
  • normal CoM (-5.0, 2.4, 5.4) Å (Sun Jan 22 09:02:36 2023)
  • reduced center failed (Sun Jan 22 09:02:36 2023)
  • volume analysis completed in 1.41 sec (Sun Jan 22 09:02:36 2023)
  • compressing 2023.jan22.5cd-3.0.mrc (Sun Jan 22 09:02:36 2023)
  • starting probe size 6.000 (Sun Jan 22 09:02:36 2023)
  • running 3v volume program (Sun Jan 22 09:02:36 2023)
  • smoothing out volume (Sun Jan 22 09:02:37 2023)
  • imaging volume (download mrc) with UCSF Chimera (Sun Jan 22 09:02:37 2023)
  • UCSF Chimera created Jmol compatible file (Sun Jan 22 09:02:48 2023)
  • compressing 2023.jan22.5cd-6.0.obj (Sun Jan 22 09:02:48 2023)
  • UCSF Chimera completed in 11.34 sec (Sun Jan 22 09:02:48 2023)
  • analyzing volume (Sun Jan 22 09:02:48 2023)
  • normal CoM (-3.1, 2.4, 3.2) Å (Sun Jan 22 09:02:49 2023)
  • reduced center failed (Sun Jan 22 09:02:50 2023)
  • volume analysis completed in 1.76 sec (Sun Jan 22 09:02:50 2023)
  • compressing 2023.jan22.5cd-6.0.mrc (Sun Jan 22 09:02:50 2023)
  • starting probe size 9.000 (Sun Jan 22 09:02:50 2023)
  • running 3v volume program (Sun Jan 22 09:02:50 2023)
  • smoothing out volume (Sun Jan 22 09:02:51 2023)
  • imaging volume (download mrc) with UCSF Chimera (Sun Jan 22 09:02:51 2023)
  • UCSF Chimera created Jmol compatible file (Sun Jan 22 09:03:01 2023)
  • compressing 2023.jan22.5cd-9.0.obj (Sun Jan 22 09:03:01 2023)
  • UCSF Chimera completed in 10.91 sec (Sun Jan 22 09:03:01 2023)
  • analyzing volume (Sun Jan 22 09:03:01 2023)
  • normal CoM (-1.0, 0.3, 3.2) Å (Sun Jan 22 09:03:03 2023)
  • reduced center failed (Sun Jan 22 09:03:04 2023)
  • volume analysis completed in 2.11 sec (Sun Jan 22 09:03:04 2023)
  • compressing 2023.jan22.5cd-9.0.mrc (Sun Jan 22 09:03:04 2023)
  • tarring file list (Sun Jan 22 09:03:04 2023)
  • compressing 2023.jan22.5cd-0.0.mrc (Sun Jan 22 09:03:04 2023)
  • compressing 2023.jan22.5cd-3.0.mrc (Sun Jan 22 09:03:04 2023)
  • compressing 2023.jan22.5cd-6.0.mrc (Sun Jan 22 09:03:04 2023)
  • compressing 2023.jan22.5cd-9.0.mrc (Sun Jan 22 09:03:04 2023)
  • FINISHED (Sun Jan 22 09:03:04 2023)

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Log file display

Show last lines of log file  
Terminal display
		
wrote to mrc file: /var/www/html/3vee/output/2023/jan22/5cd/2023.jan22.5cd-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 2023.jan22.5cd-9.0.obj 
Message: UCSF Chimera completed in 10.91 sec 
OBJFILE /var/www/html/3vee/output/2023/jan22/5cd/2023.jan22.5cd-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-1.0, 0.3, 3.2) Å 
Message: reduced center failed 
Message: volume analysis completed in 2.11 sec 
Message: compressing 2023.jan22.5cd-9.0.mrc 
Message: tarring file list 
Message: compressing 2023.jan22.5cd-0.0.mrc 
Message: compressing 2023.jan22.5cd-3.0.mrc 
Message: compressing 2023.jan22.5cd-6.0.mrc 
Message: compressing 2023.jan22.5cd-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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