3v Running Log for JobId '2019.dec02.382'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=130.179.244.50 (Mon Dec 2 17:57:20 2019)
  • converting pdb into xyzr (Mon Dec 2 17:57:20 2019)
  • completed conversion of PDB file: 2019.dec02.382.pdb (size: 237k) (Mon Dec 2 17:57:26 2019)
  • converted 7576 atoms of 7576 atoms (Mon Dec 2 17:57:26 2019)
  • found 7576 atoms in pdb (Mon Dec 2 17:57:26 2019)
  • running 3v all channel program (Mon Dec 2 17:57:26 2019)
  • created 8 channel files (Mon Dec 2 17:57:32 2019)
  • Download MRC files: 1 2 3 4 5 6 7 8 (Mon Dec 2 17:57:32 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 17:57:32 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 18:03:02 2019)
  • compressing channel-001.obj (Mon Dec 2 18:03:02 2019)
  • UCSF Chimera completed in 5 min 30 sec (Mon Dec 2 18:03:02 2019)
  • analyzing volume (Mon Dec 2 18:03:02 2019)
  • normal CoM (-51.6, -49.2, -36.9) Å (Mon Dec 2 18:03:02 2019)
  • reduced center failed (Mon Dec 2 18:03:02 2019)
  • volume analysis completed in 23.11 msec (Mon Dec 2 18:03:02 2019)
  • compressing channel-001.mrc (Mon Dec 2 18:03:02 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 18:03:02 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 18:08:30 2019)
  • compressing channel-002.obj (Mon Dec 2 18:08:30 2019)
  • UCSF Chimera completed in 5 min 28 sec (Mon Dec 2 18:08:30 2019)
  • analyzing volume (Mon Dec 2 18:08:30 2019)
  • normal CoM (-51.6, -47.4, -38.6) Å (Mon Dec 2 18:08:30 2019)
  • reduced center failed (Mon Dec 2 18:08:30 2019)
  • volume analysis completed in 22.81 msec (Mon Dec 2 18:08:30 2019)
  • compressing channel-002.mrc (Mon Dec 2 18:08:30 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 18:08:30 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 18:13:58 2019)
  • compressing channel-003.obj (Mon Dec 2 18:13:58 2019)
  • UCSF Chimera completed in 5 min 28 sec (Mon Dec 2 18:13:58 2019)
  • analyzing volume (Mon Dec 2 18:13:58 2019)
  • normal CoM (-51.6, -48.6, -38.7) Å (Mon Dec 2 18:13:58 2019)
  • reduced center failed (Mon Dec 2 18:13:58 2019)
  • volume analysis completed in 22.98 msec (Mon Dec 2 18:13:58 2019)
  • compressing channel-003.mrc (Mon Dec 2 18:13:58 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 18:13:58 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 18:19:26 2019)
  • compressing channel-004.obj (Mon Dec 2 18:19:26 2019)
  • UCSF Chimera completed in 5 min 29 sec (Mon Dec 2 18:19:27 2019)
  • analyzing volume (Mon Dec 2 18:19:27 2019)
  • normal CoM (-51.6, -49.1, -38.1) Å (Mon Dec 2 18:19:27 2019)
  • reduced center failed (Mon Dec 2 18:19:27 2019)
  • volume analysis completed in 22.69 msec (Mon Dec 2 18:19:27 2019)
  • compressing channel-004.mrc (Mon Dec 2 18:19:27 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 18:19:27 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 18:24:53 2019)
  • compressing channel-005.obj (Mon Dec 2 18:24:53 2019)
  • UCSF Chimera completed in 5 min 27 sec (Mon Dec 2 18:24:53 2019)
  • analyzing volume (Mon Dec 2 18:24:53 2019)
  • normal CoM (-48.7, -48.5, -39.2) Å (Mon Dec 2 18:24:53 2019)
  • reduced center failed (Mon Dec 2 18:24:53 2019)
  • volume analysis completed in 31.81 msec (Mon Dec 2 18:24:53 2019)
  • compressing channel-005.mrc (Mon Dec 2 18:24:53 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 18:24:53 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 18:30:19 2019)
  • compressing channel-006.obj (Mon Dec 2 18:30:19 2019)
  • UCSF Chimera completed in 5 min 25 sec (Mon Dec 2 18:30:19 2019)
  • analyzing volume (Mon Dec 2 18:30:19 2019)
  • normal CoM (-48.7, -50.8, -38.0) Å (Mon Dec 2 18:30:19 2019)
  • reduced center failed (Mon Dec 2 18:30:19 2019)
  • volume analysis completed in 32.33 msec (Mon Dec 2 18:30:19 2019)
  • compressing channel-006.mrc (Mon Dec 2 18:30:19 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 18:30:19 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 18:35:47 2019)
  • compressing channel-007.obj (Mon Dec 2 18:35:47 2019)
  • UCSF Chimera completed in 5 min 29 sec (Mon Dec 2 18:35:48 2019)
  • analyzing volume (Mon Dec 2 18:35:48 2019)
  • normal CoM (-48.7, -49.7, -37.0) Å (Mon Dec 2 18:35:48 2019)
  • reduced center failed (Mon Dec 2 18:35:48 2019)
  • volume analysis completed in 31.89 msec (Mon Dec 2 18:35:48 2019)
  • compressing channel-007.mrc (Mon Dec 2 18:35:48 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 18:35:48 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 18:41:13 2019)
  • compressing channel-008.obj (Mon Dec 2 18:41:13 2019)
  • UCSF Chimera completed in 5 min 25 sec (Mon Dec 2 18:41:13 2019)
  • analyzing volume (Mon Dec 2 18:41:13 2019)
  • normal CoM (-48.7, -47.5, -40.3) Å (Mon Dec 2 18:41:13 2019)
  • reduced center failed (Mon Dec 2 18:41:13 2019)
  • volume analysis completed in 31.75 msec (Mon Dec 2 18:41:13 2019)
  • compressing channel-008.mrc (Mon Dec 2 18:41:13 2019)
  • tarring file list (Mon Dec 2 18:41:13 2019)
  • compressing channel-001.mrc (Mon Dec 2 18:41:13 2019)

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Log file display

Show last lines of log file 
Terminal display
		
Message: analyzing volume 
Message: normal CoM (-48.7, -47.5, -40.3) Å 
Message: reduced center failed 
Message: volume analysis completed in 31.75 msec 
Message: compressing channel-008.mrc 
Message: tarring file list 
Message: compressing channel-001.mrc 
Traceback (most recent call last): 
File "/var/www/html/3vee/py/runChannelFinder.py", line 67, in  
runthreev.start() 
File "/var/www/html/3vee/py/runChannelFinder.py", line 57, in start 
self.threev.webMrcSection(mrcfiles, self.website, f, pdb=True, pymol=self.params['pymol']) 
File "/var/www/html/py/ThreeVLib.py", line 1033, in webMrcSection 
gzmrcfile = self.gzipFile(mrcfile, pymol) 
File "/var/www/html/py/ThreeVLib.py", line 853, in gzipFile 
header = mrc.readHeaderFromFile(fname) 
File "/var/www/html/py/pyami/mrc.py", line 666, in readHeaderFromFile 
f = open(filename) 
IOError: [Errno 2] No such file or directory: '/var/www/html/3vee/output/2019/dec02/382/channel-001.mrc' 

		


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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