3v Running Log for JobId '2020.feb11.e55'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=165.190.89.172 (Tue Feb 11 12:59:06 2020)
  • downloading pdb file (Tue Feb 11 12:59:06 2020)
  • failed to download pdb id: 2lyz (Tue Feb 11 12:59:06 2020)
  • trying download pdb id again without bio unit (Tue Feb 11 12:59:08 2020)
  • completed download of PDB id 2lyz (size: 130 k, 1648 lines) (Tue Feb 11 12:59:08 2020)
  • converting pdb into xyzr (Tue Feb 11 12:59:08 2020)
  • completed conversion of PDB file: 2lyz-2020.feb11.e55.pdb (size: 31k) (Tue Feb 11 12:59:09 2020)
  • converted 1001 atoms of 1001 atoms (Tue Feb 11 12:59:09 2020)
  • found 1001 atoms in pdb (Tue Feb 11 12:59:09 2020)
  • starting probe size 0.000 (Tue Feb 11 12:59:09 2020)
  • running 3v volume program (Tue Feb 11 12:59:09 2020)
  • smoothing out volume (Tue Feb 11 12:59:09 2020)
  • imaging volume (download mrc) with UCSF Chimera (Tue Feb 11 12:59:09 2020)
  • UCSF Chimera created Jmol compatible file (Tue Feb 11 12:59:17 2020)
  • compressing 2lyz-2020.feb11.e55-0.0.obj (Tue Feb 11 12:59:17 2020)
  • UCSF Chimera completed in 7.9 sec (Tue Feb 11 12:59:17 2020)
  • analyzing volume (Tue Feb 11 12:59:17 2020)
  • normal CoM (1.2, -1.5, -4.7) Å (Tue Feb 11 12:59:20 2020)
  • reduced center failed (Tue Feb 11 12:59:20 2020)
  • volume analysis completed in 2.98 sec (Tue Feb 11 12:59:20 2020)
  • compressing 2lyz-2020.feb11.e55-0.0.mrc (Tue Feb 11 12:59:20 2020)
  • starting probe size 3.000 (Tue Feb 11 12:59:20 2020)
  • running 3v volume program (Tue Feb 11 12:59:20 2020)
  • smoothing out volume (Tue Feb 11 12:59:21 2020)
  • imaging volume (download mrc) with UCSF Chimera (Tue Feb 11 12:59:21 2020)
  • UCSF Chimera created Jmol compatible file (Tue Feb 11 12:59:28 2020)
  • compressing 2lyz-2020.feb11.e55-3.0.obj (Tue Feb 11 12:59:28 2020)
  • UCSF Chimera completed in 7.62 sec (Tue Feb 11 12:59:28 2020)
  • analyzing volume (Tue Feb 11 12:59:28 2020)
  • normal CoM (2.3, -3.5, -4.6) Å (Tue Feb 11 12:59:32 2020)
  • reduced center failed (Tue Feb 11 12:59:33 2020)
  • volume analysis completed in 4.72 sec (Tue Feb 11 12:59:33 2020)
  • compressing 2lyz-2020.feb11.e55-3.0.mrc (Tue Feb 11 12:59:33 2020)
  • starting probe size 6.000 (Tue Feb 11 12:59:33 2020)
  • running 3v volume program (Tue Feb 11 12:59:33 2020)
  • smoothing out volume (Tue Feb 11 12:59:35 2020)
  • imaging volume (download mrc) with UCSF Chimera (Tue Feb 11 12:59:35 2020)
  • UCSF Chimera created Jmol compatible file (Tue Feb 11 12:59:43 2020)
  • compressing 2lyz-2020.feb11.e55-6.0.obj (Tue Feb 11 12:59:43 2020)
  • UCSF Chimera completed in 7.84 sec (Tue Feb 11 12:59:43 2020)
  • analyzing volume (Tue Feb 11 12:59:43 2020)
  • normal CoM (1.5, -2.5, -4.6) Å (Tue Feb 11 12:59:48 2020)
  • reduced center failed (Tue Feb 11 12:59:49 2020)
  • volume analysis completed in 6.11 sec (Tue Feb 11 12:59:49 2020)
  • compressing 2lyz-2020.feb11.e55-6.0.mrc (Tue Feb 11 12:59:49 2020)
  • starting probe size 9.000 (Tue Feb 11 12:59:49 2020)
  • running 3v volume program (Tue Feb 11 12:59:49 2020)
  • smoothing out volume (Tue Feb 11 12:59:53 2020)
  • imaging volume (download mrc) with UCSF Chimera (Tue Feb 11 12:59:53 2020)
  • UCSF Chimera created Jmol compatible file (Tue Feb 11 13:00:01 2020)
  • compressing 2lyz-2020.feb11.e55-9.0.obj (Tue Feb 11 13:00:01 2020)
  • UCSF Chimera completed in 8.28 sec (Tue Feb 11 13:00:02 2020)
  • analyzing volume (Tue Feb 11 13:00:02 2020)
  • normal CoM (2.5, -3.4, -4.5) Å (Tue Feb 11 13:00:08 2020)
  • reduced center failed (Tue Feb 11 13:00:10 2020)
  • volume analysis completed in 8.29 sec (Tue Feb 11 13:00:10 2020)
  • compressing 2lyz-2020.feb11.e55-9.0.mrc (Tue Feb 11 13:00:10 2020)
  • tarring file list (Tue Feb 11 13:00:10 2020)
  • compressing 2lyz-2020.feb11.e55-0.0.mrc (Tue Feb 11 13:00:10 2020)
  • compressing 2lyz-2020.feb11.e55-3.0.mrc (Tue Feb 11 13:00:10 2020)
  • compressing 2lyz-2020.feb11.e55-6.0.mrc (Tue Feb 11 13:00:10 2020)
  • compressing 2lyz-2020.feb11.e55-9.0.mrc (Tue Feb 11 13:00:10 2020)
  • FINISHED (Tue Feb 11 13:00:10 2020)

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Log file display

Show last lines of log file 
Terminal display
		
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2lyz-2020.feb11.e55-9.0.obj 
Message: UCSF Chimera completed in 8.28 sec 
OBJFILE /var/www/html/3vee/output/2020/feb11/e55/2lyz-2020.feb11.e55-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (2.5, -3.4, -4.5) Å 
Message: reduced center failed 
Message: volume analysis completed in 8.29 sec 
Message: compressing 2lyz-2020.feb11.e55-9.0.mrc 
Message: tarring file list 
Message: compressing 2lyz-2020.feb11.e55-0.0.mrc 
Message: compressing 2lyz-2020.feb11.e55-3.0.mrc 
Message: compressing 2lyz-2020.feb11.e55-6.0.mrc 
Message: ... rundir: 
/var/www/html/3vee/output/2020/feb11/e55 
COMPLETE SCRIPT:	64.36 sec 
compressing 2lyz-2020.feb11.e55-9.0.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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