3v Running Log for JobId '2022.sep22.cfa'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=132.247.249.242 (Thu Sep 22 09:11:13 2022)
  • waiting for system load (2.13) to calm down, total wait time: 1.54 sec (Thu Sep 22 09:11:13 2022)
  • running now (Thu Sep 22 09:11:15 2022)
  • downloading pdb file (Thu Sep 22 09:11:15 2022)
  • waiting for system load (2.12) to calm down, total wait time: 3.05 sec (Thu Sep 22 09:11:15 2022)
  • running now (Thu Sep 22 09:11:16 2022)
  • waiting for system load (2.12) to calm down, total wait time: 4.55 sec (Thu Sep 22 09:11:16 2022)
  • running now (Thu Sep 22 09:11:18 2022)
  • completed download of PDB id 1HKB (size: 592 k, 7490 lines) (Thu Sep 22 09:11:18 2022)
  • waiting for system load (2.12) to calm down, total wait time: 6.06 sec (Thu Sep 22 09:11:18 2022)
  • running now (Thu Sep 22 09:11:19 2022)
  • converting pdb into xyzr (Thu Sep 22 09:11:19 2022)
  • waiting for system load (2.27) to calm down, total wait time: 8.21 sec (Thu Sep 22 09:11:19 2022)
  • running now (Thu Sep 22 09:11:22 2022)
  • completed conversion of PDB file: 1HKB-2022.sep22.cfa.pdb (size: 220k) (Thu Sep 22 09:11:27 2022)
  • converted 7032 atoms of 7032 atoms (Thu Sep 22 09:11:27 2022)
  • found 7032 atoms in pdb (Thu Sep 22 09:11:27 2022)
  • waiting for system load (2.33) to calm down, total wait time: 10.66 sec (Thu Sep 22 09:11:27 2022)
  • running now (Thu Sep 22 09:11:29 2022)
  • running 3v volume program (Thu Sep 22 09:11:29 2022)
  • waiting for system load (2.33) to calm down, total wait time: 13.11 sec (Thu Sep 22 09:11:29 2022)
  • running now (Thu Sep 22 09:11:31 2022)
  • waiting for system load (2.95) to calm down, total wait time: 20.63 sec (Thu Sep 22 09:11:40 2022)
  • waiting for system load (2.88) to calm down, total wait time: 27.37 sec (Thu Sep 22 09:11:47 2022)
  • running now (Thu Sep 22 09:11:54 2022)
  • trimming mrc volume (Thu Sep 22 09:11:54 2022)
  • waiting for system load (2.59) to calm down, total wait time: 31.49 sec (Thu Sep 22 09:11:54 2022)
  • waiting for system load (2.59) to calm down, total wait time: 35.61 sec (Thu Sep 22 09:11:58 2022)
  • running now (Thu Sep 22 09:12:02 2022)
  • trimmed MRC file: /var/www/html/3vee/output/2022/sep22/cfa/1HKB-2022.sep22.cfa-trim.mrc (Thu Sep 22 09:12:03 2022)
  • imaging volume (download mrc) with UCSF Chimera (Thu Sep 22 09:12:03 2022)
  • UCSF Chimera created 3D printing compatible file (Thu Sep 22 09:12:08 2022)
  • UCSF Chimera completed in 4.73 sec (Thu Sep 22 09:12:08 2022)
  • analyzing volume (Thu Sep 22 09:12:08 2022)
  • normal CoM (5.8, -2.7, -18.1) Å (Thu Sep 22 09:12:13 2022)
  • reduced center failed (Thu Sep 22 09:12:14 2022)
  • volume analysis completed in 6.82 sec (Thu Sep 22 09:12:14 2022)
  • waiting for system load (2.71) to calm down, total wait time: 40.71 sec (Thu Sep 22 09:12:14 2022)
  • waiting for system load (2.65) to calm down, total wait time: 45.3 sec (Thu Sep 22 09:12:19 2022)
  • running now (Thu Sep 22 09:12:24 2022)
  • Created virtual frame buffer on port :1312 (Thu Sep 22 09:12:24 2022)
  • Please wait: Quadraitc decimating x3d volume and converting to STL using meshlab (Thu Sep 22 09:12:24 2022)
  • waiting for system load (2.65) to calm down, total wait time: 49.89 sec (Thu Sep 22 09:12:24 2022)
  • waiting for system load (2.60) to calm down, total wait time: 54.09 sec (Thu Sep 22 09:12:29 2022)
  • running now (Thu Sep 22 09:12:33 2022)
  • decimated STL file: /var/www/html/3vee/output/2022/sep22/cfa/1HKB-2022.sep22.cfa-trim.stl (Thu Sep 22 09:12:35 2022)
  • MeshLab completed in 20.6 sec (Thu Sep 22 09:12:35 2022)
  • FINISHED (Thu Sep 22 09:12:35 2022)

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Log file display

Show last lines of log file 
Terminal display
		
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created 3D printing compatible file 
Message: UCSF Chimera completed in 4.73 sec 
Message: analyzing volume 
Message: normal CoM (5.8, -2.7, -18.1) Å 
Message: reduced center failed 
Message: volume analysis completed in 6.82 sec 
Message: waiting for system load (2.71) to calm down, total wait time: 40.71 sec 
Message: waiting for system load (2.65) to calm down, total wait time: 45.3 sec 
Message: running now 
Message: Created virtual frame buffer on port :1312 
Message: Please wait: Quadraitc decimating x3d volume and converting to STL using meshlab 
Message: waiting for system load (2.65) to calm down, total wait time: 49.89 sec 
Message: waiting for system load (2.60) to calm down, total wait time: 54.09 sec 
Message: running now 
Message: decimated STL file: /var/www/html/3vee/output/2022/sep22/cfa/1HKB-2022.sep22.cfa-trim.stl 
Message: MeshLab completed in 20.6 sec 
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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