3v Running Log for JobId '2018.may16.e75'

Program is still running, progress is shown below

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  • host ip address=172.85.57.129 (Wed May 16 12:19:38 2018)
  • converting pdb into xyzr (Wed May 16 12:19:38 2018)
  • completed conversion of PDB file: 2018.may16.e75.pdb (size: 334k) (Wed May 16 12:19:46 2018)
  • converted 10679 atoms of 10679 atoms (Wed May 16 12:19:46 2018)
  • found 10679 atoms in pdb (Wed May 16 12:19:46 2018)
  • running 3v all channel program (Wed May 16 12:19:46 2018)
  • created 2 channel files (Wed May 16 12:19:50 2018)
  • Download MRC files: 1 2 (Wed May 16 12:19:50 2018)
  • imaging volume (download mrc) with UCSF Chimera (Wed May 16 12:19:50 2018)
  • UCSF Chimera created Jmol compatible file (Wed May 16 12:19:55 2018)
  • compressing channel-001.obj (Wed May 16 12:19:55 2018)
  • UCSF Chimera completed in 5.4 sec (Wed May 16 12:19:56 2018)
  • analyzing volume (Wed May 16 12:19:56 2018)
  • normal CoM (-58.8, -60.8, -75.6) Å (Wed May 16 12:19:56 2018)
  • reduced center failed (Wed May 16 12:19:56 2018)
  • volume analysis completed in 260.09 msec (Wed May 16 12:19:56 2018)
  • compressing channel-001.mrc (Wed May 16 12:19:56 2018)
  • imaging volume (download mrc) with UCSF Chimera (Wed May 16 12:19:56 2018)
  • UCSF Chimera created Jmol compatible file (Wed May 16 12:20:01 2018)
  • compressing channel-002.obj (Wed May 16 12:20:01 2018)
  • UCSF Chimera completed in 4.71 sec (Wed May 16 12:20:01 2018)
  • analyzing volume (Wed May 16 12:20:01 2018)
  • normal CoM (-71.1, -70.2, -83.5) Å (Wed May 16 12:20:01 2018)
  • reduced center failed (Wed May 16 12:20:01 2018)
  • volume analysis completed in 43.47 msec (Wed May 16 12:20:01 2018)
  • compressing channel-002.mrc (Wed May 16 12:20:01 2018)
  • tarring file list (Wed May 16 12:20:01 2018)
  • compressing channel-001.mrc (Wed May 16 12:20:01 2018)

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Log file display

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Terminal display
		
Message: analyzing volume 
Message: normal CoM (-71.1, -70.2, -83.5) Å 
Message: reduced center failed 
Message: volume analysis completed in 43.47 msec 
Message: compressing channel-002.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/2018/may16/e75/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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