3v Running Log for JobId '2020.oct16.1d3'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=14.139.221.148 (Fri Oct 16 07:19:20 2020)
  • converting pdb into xyzr (Fri Oct 16 07:19:20 2020)
  • completed conversion of PDB file: 2020.oct16.1d3.pdb (size: 126k) (Fri Oct 16 07:19:23 2020)
  • converted 4017 atoms of 4017 atoms (Fri Oct 16 07:19:23 2020)
  • found 4017 atoms in pdb (Fri Oct 16 07:19:23 2020)
  • running 3v all channel program (Fri Oct 16 07:19:23 2020)
  • created 2 channel files (Fri Oct 16 07:19:25 2020)
  • Download MRC files: 1 2 (Fri Oct 16 07:19:25 2020)
  • imaging volume (download mrc) with UCSF Chimera (Fri Oct 16 07:19:25 2020)
  • UCSF Chimera created Jmol compatible file (Fri Oct 16 07:19:30 2020)
  • compressing channel-001.obj (Fri Oct 16 07:19:30 2020)
  • UCSF Chimera completed in 5.06 sec (Fri Oct 16 07:19:30 2020)
  • analyzing volume (Fri Oct 16 07:19:30 2020)
  • normal CoM (-34.0, -40.0, -44.8) Å (Fri Oct 16 07:19:30 2020)
  • reduced center failed (Fri Oct 16 07:19:30 2020)
  • volume analysis completed in 86.87 msec (Fri Oct 16 07:19:30 2020)
  • compressing channel-001.pdb (Fri Oct 16 07:19:30 2020)
  • compressing channel-001.mrc (Fri Oct 16 07:19:30 2020)
  • imaging volume (download mrc) with UCSF Chimera (Fri Oct 16 07:19:30 2020)
  • UCSF Chimera created Jmol compatible file (Fri Oct 16 07:19:34 2020)
  • compressing channel-002.obj (Fri Oct 16 07:19:34 2020)
  • UCSF Chimera completed in 3.8 sec (Fri Oct 16 07:19:34 2020)
  • analyzing volume (Fri Oct 16 07:19:34 2020)
  • normal CoM (-43.4, -44.8, -43.1) Å (Fri Oct 16 07:19:34 2020)
  • reduced center failed (Fri Oct 16 07:19:34 2020)
  • volume analysis completed in 34.85 msec (Fri Oct 16 07:19:34 2020)
  • compressing channel-002.pdb (Fri Oct 16 07:19:34 2020)
  • compressing channel-002.mrc (Fri Oct 16 07:19:34 2020)
  • tarring file list (Fri Oct 16 07:19:34 2020)
  • compressing channel-001.pdb (Fri Oct 16 07:19:34 2020)
  • compressing channel-001.mrc (Fri Oct 16 07:19:34 2020)

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Log file display

Show last lines of log file 
Terminal display
		
Message: reduced center failed 
Message: volume analysis completed in 34.85 msec 
Message: compressing channel-002.pdb 
Message: compressing channel-002.mrc 
Message: tarring file list 
Message: compressing channel-001.pdb 
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/2020/oct16/1d3/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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