3v Running Log for JobId '2022.jun23.932'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=193.136.35.65 (Thu Jun 23 11:32:47 2022)
  • converting pdb into xyzr (Thu Jun 23 11:32:48 2022)
  • completed conversion of PDB file: 2022.jun23.932.pdb (size: 178k) (Thu Jun 23 11:32:50 2022)
  • converted 5683 atoms of 5683 atoms (Thu Jun 23 11:32:50 2022)
  • found 5683 atoms in pdb (Thu Jun 23 11:32:50 2022)
  • running 3v all channel program (Thu Jun 23 11:32:50 2022)
  • created 5 channel files (Thu Jun 23 11:33:12 2022)
  • Download MRC files: 1 2 3 4 5 (Thu Jun 23 11:33:12 2022)
  • imaging volume (download mrc) with UCSF Chimera (Thu Jun 23 11:33:12 2022)
  • UCSF Chimera created Jmol compatible file (Thu Jun 23 11:33:17 2022)
  • compressing channel-001.obj (Thu Jun 23 11:33:17 2022)
  • UCSF Chimera completed in 5.53 sec (Thu Jun 23 11:33:17 2022)
  • analyzing volume (Thu Jun 23 11:33:17 2022)
  • normal CoM (-20.4, -35.2, -55.1) Å (Thu Jun 23 11:33:18 2022)
  • reduced center failed (Thu Jun 23 11:33:18 2022)
  • volume analysis completed in 0.88 sec (Thu Jun 23 11:33:18 2022)
  • compressing channel-001.pdb (Thu Jun 23 11:33:18 2022)
  • compressing channel-001.mrc (Thu Jun 23 11:33:19 2022)
  • imaging volume (download mrc) with UCSF Chimera (Thu Jun 23 11:33:19 2022)
  • UCSF Chimera created Jmol compatible file (Thu Jun 23 11:33:22 2022)
  • compressing channel-002.obj (Thu Jun 23 11:33:22 2022)
  • UCSF Chimera completed in 3.49 sec (Thu Jun 23 11:33:22 2022)
  • analyzing volume (Thu Jun 23 11:33:22 2022)
  • normal CoM (-34.1, -46.5, -64.1) Å (Thu Jun 23 11:33:22 2022)
  • reduced center failed (Thu Jun 23 11:33:22 2022)
  • volume analysis completed in 99.68 msec (Thu Jun 23 11:33:22 2022)
  • compressing channel-002.pdb (Thu Jun 23 11:33:22 2022)
  • compressing channel-002.mrc (Thu Jun 23 11:33:22 2022)
  • imaging volume (download mrc) with UCSF Chimera (Thu Jun 23 11:33:22 2022)
  • UCSF Chimera created Jmol compatible file (Thu Jun 23 11:33:26 2022)
  • compressing channel-003.obj (Thu Jun 23 11:33:26 2022)
  • UCSF Chimera completed in 3.72 sec (Thu Jun 23 11:33:26 2022)
  • analyzing volume (Thu Jun 23 11:33:26 2022)
  • normal CoM (-30.7, -45.0, -63.1) Å (Thu Jun 23 11:33:26 2022)
  • reduced center failed (Thu Jun 23 11:33:26 2022)
  • volume analysis completed in 163.93 msec (Thu Jun 23 11:33:26 2022)
  • compressing channel-003.pdb (Thu Jun 23 11:33:26 2022)
  • compressing channel-003.mrc (Thu Jun 23 11:33:26 2022)
  • imaging volume (download mrc) with UCSF Chimera (Thu Jun 23 11:33:26 2022)
  • UCSF Chimera created Jmol compatible file (Thu Jun 23 11:33:30 2022)
  • compressing channel-004.obj (Thu Jun 23 11:33:30 2022)
  • UCSF Chimera completed in 3.53 sec (Thu Jun 23 11:33:30 2022)
  • analyzing volume (Thu Jun 23 11:33:30 2022)
  • normal CoM (-27.1, -46.9, -65.1) Å (Thu Jun 23 11:33:30 2022)
  • reduced center failed (Thu Jun 23 11:33:30 2022)
  • volume analysis completed in 83.47 msec (Thu Jun 23 11:33:30 2022)
  • compressing channel-004.pdb (Thu Jun 23 11:33:30 2022)
  • compressing channel-004.mrc (Thu Jun 23 11:33:30 2022)
  • imaging volume (download mrc) with UCSF Chimera (Thu Jun 23 11:33:30 2022)
  • UCSF Chimera created Jmol compatible file (Thu Jun 23 11:33:33 2022)
  • compressing channel-005.obj (Thu Jun 23 11:33:33 2022)
  • UCSF Chimera completed in 3.38 sec (Thu Jun 23 11:33:34 2022)
  • analyzing volume (Thu Jun 23 11:33:34 2022)
  • normal CoM (-36.5, -46.1, -63.4) Å (Thu Jun 23 11:33:34 2022)
  • reduced center failed (Thu Jun 23 11:33:34 2022)
  • volume analysis completed in 45.3 msec (Thu Jun 23 11:33:34 2022)
  • compressing channel-005.pdb (Thu Jun 23 11:33:34 2022)
  • compressing channel-005.mrc (Thu Jun 23 11:33:34 2022)
  • tarring file list (Thu Jun 23 11:33:34 2022)
  • compressing channel-001.pdb (Thu Jun 23 11:33:34 2022)
  • compressing channel-001.mrc (Thu Jun 23 11:33:34 2022)
  • compressing channel-002.pdb (Thu Jun 23 11:33:34 2022)
  • compressing channel-002.mrc (Thu Jun 23 11:33:34 2022)
  • compressing channel-003.pdb (Thu Jun 23 11:33:34 2022)
  • compressing channel-003.mrc (Thu Jun 23 11:33:34 2022)
  • compressing channel-004.pdb (Thu Jun 23 11:33:34 2022)
  • compressing channel-004.mrc (Thu Jun 23 11:33:34 2022)
  • compressing channel-005.pdb (Thu Jun 23 11:33:34 2022)
  • compressing channel-005.mrc (Thu Jun 23 11:33:34 2022)
  • FINISHED (Thu Jun 23 11:33:34 2022)

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Log file display

Show last lines of log file  
Terminal display
		
channel-001.mrc.gz 
channel-002.mrc.gz 
channel-003.mrc.gz 
channel-004.mrc.gz 
channel-005.mrc.gz 
... rundir: 
/var/www/html/3vee/output/2022/jun23/932 
COMPLETE SCRIPT:	46.3 sec 
Message: tarring file list 
Message: compressing channel-001.pdb 
Message: compressing channel-001.mrc 
Message: compressing channel-002.pdb 
Message: compressing channel-002.mrc 
Message: compressing channel-003.pdb 
Message: compressing channel-003.mrc 
Message: compressing channel-004.pdb 
Message: compressing channel-004.mrc 
Message: compressing channel-005.pdb 
Message: compressing channel-005.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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