3v Running Log for JobId '2020.sep15.7b9'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=193.54.246.71 (Tue Sep 15 10:26:21 2020)
  • converting pdb into xyzr (Tue Sep 15 10:26:21 2020)
  • completed conversion of PDB file: 2020.sep15.7b9.pdb (size: 138k) (Tue Sep 15 10:26:24 2020)
  • converted 4422 atoms of 4422 atoms (Tue Sep 15 10:26:24 2020)
  • found 4422 atoms in pdb (Tue Sep 15 10:26:24 2020)
  • starting probe size 0.000 (Tue Sep 15 10:26:24 2020)
  • running 3v volume program (Tue Sep 15 10:26:24 2020)
  • smoothing out volume (Tue Sep 15 10:26:25 2020)
  • imaging volume (download mrc) with UCSF Chimera (Tue Sep 15 10:26:25 2020)
  • UCSF Chimera created Jmol compatible file (Tue Sep 15 10:26:33 2020)
  • compressing 2020.sep15.7b9-0.0.obj (Tue Sep 15 10:26:33 2020)
  • UCSF Chimera completed in 9.1 sec (Tue Sep 15 10:26:34 2020)
  • analyzing volume (Tue Sep 15 10:26:34 2020)
  • normal CoM (12.7, -3.7, -14.0) Å (Tue Sep 15 10:26:35 2020)
  • reduced center failed (Tue Sep 15 10:26:35 2020)
  • volume analysis completed in 1.73 sec (Tue Sep 15 10:26:35 2020)
  • compressing 2020.sep15.7b9-0.0.mrc (Tue Sep 15 10:26:35 2020)
  • starting probe size 3.000 (Tue Sep 15 10:26:36 2020)
  • running 3v volume program (Tue Sep 15 10:26:36 2020)
  • smoothing out volume (Tue Sep 15 10:26:36 2020)
  • imaging volume (download mrc) with UCSF Chimera (Tue Sep 15 10:26:36 2020)
  • UCSF Chimera created Jmol compatible file (Tue Sep 15 10:26:46 2020)
  • compressing 2020.sep15.7b9-3.0.obj (Tue Sep 15 10:26:46 2020)
  • UCSF Chimera completed in 10.41 sec (Tue Sep 15 10:26:46 2020)
  • analyzing volume (Tue Sep 15 10:26:46 2020)
  • normal CoM (12.6, -5.6, -11.9) Å (Tue Sep 15 10:26:48 2020)
  • reduced center failed (Tue Sep 15 10:26:49 2020)
  • volume analysis completed in 2.38 sec (Tue Sep 15 10:26:49 2020)
  • compressing 2020.sep15.7b9-3.0.mrc (Tue Sep 15 10:26:49 2020)
  • starting probe size 6.000 (Tue Sep 15 10:26:49 2020)
  • running 3v volume program (Tue Sep 15 10:26:49 2020)
  • smoothing out volume (Tue Sep 15 10:26:49 2020)
  • imaging volume (download mrc) with UCSF Chimera (Tue Sep 15 10:26:49 2020)
  • UCSF Chimera created Jmol compatible file (Tue Sep 15 10:26:59 2020)
  • compressing 2020.sep15.7b9-6.0.obj (Tue Sep 15 10:26:59 2020)
  • UCSF Chimera completed in 9.51 sec (Tue Sep 15 10:26:59 2020)
  • analyzing volume (Tue Sep 15 10:26:59 2020)
  • normal CoM (10.6, -5.5, -13.9) Å (Tue Sep 15 10:27:01 2020)
  • reduced center failed (Tue Sep 15 10:27:02 2020)
  • volume analysis completed in 2.8 sec (Tue Sep 15 10:27:02 2020)
  • compressing 2020.sep15.7b9-6.0.mrc (Tue Sep 15 10:27:02 2020)
  • starting probe size 9.000 (Tue Sep 15 10:27:02 2020)
  • running 3v volume program (Tue Sep 15 10:27:02 2020)
  • smoothing out volume (Tue Sep 15 10:27:03 2020)
  • imaging volume (download mrc) with UCSF Chimera (Tue Sep 15 10:27:03 2020)
  • UCSF Chimera created Jmol compatible file (Tue Sep 15 10:27:12 2020)
  • compressing 2020.sep15.7b9-9.0.obj (Tue Sep 15 10:27:12 2020)
  • UCSF Chimera completed in 9.06 sec (Tue Sep 15 10:27:12 2020)
  • analyzing volume (Tue Sep 15 10:27:12 2020)
  • normal CoM (8.6, -3.5, -11.9) Å (Tue Sep 15 10:27:15 2020)
  • reduced center failed (Tue Sep 15 10:27:15 2020)
  • volume analysis completed in 3.17 sec (Tue Sep 15 10:27:15 2020)
  • compressing 2020.sep15.7b9-9.0.mrc (Tue Sep 15 10:27:15 2020)
  • tarring file list (Tue Sep 15 10:27:15 2020)
  • compressing 2020.sep15.7b9-0.0.mrc (Tue Sep 15 10:27:15 2020)
  • compressing 2020.sep15.7b9-3.0.mrc (Tue Sep 15 10:27:15 2020)
  • compressing 2020.sep15.7b9-6.0.mrc (Tue Sep 15 10:27:15 2020)
  • compressing 2020.sep15.7b9-9.0.mrc (Tue Sep 15 10:27:15 2020)
  • FINISHED (Tue Sep 15 10:27:15 2020)

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Log file display

Show last lines of log file 
Terminal display
		
wrote to mrc file: /var/www/html/3vee/output/2020/sep15/7b9/2020.sep15.7b9-9.0.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 2020.sep15.7b9-9.0.obj 
Message: UCSF Chimera completed in 9.06 sec 
OBJFILE /var/www/html/3vee/output/2020/sep15/7b9/2020.sep15.7b9-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (8.6, -3.5, -11.9) Å 
Message: reduced center failed 
Message: volume analysis completed in 3.17 sec 
Message: compressing 2020.sep15.7b9-9.0.mrc 
Message: tarring file list 
Message: compressing 2020.sep15.7b9-0.0.mrc 
Message: compressing 2020.sep15.7b9-3.0.mrc 
Message: compressing 2020.sep15.7b9-6.0.mrc 
Message: compressing 2020.sep15.7b9-9.0.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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