Thread: [Biskit-general] How to setup biskit to use SurfaceRacer instead WhatIf
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From: OOMMEN KM <oom...@gm...> - 2013-09-04 06:58:39
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Hi, Please help to make my Biskit installation to use SurfaceRacer instead WhatIf. Oommen Mathew |
From: Raik G. <rai...@gm...> - 2013-09-04 12:09:33
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Hi Oommen, whatif is not really supported by Biskit any longer. We just left the module in place, in case people want to play around with it or update it themselves. The installation of Surface Racer for Biskit is described here: http://biskit.pasteur.fr/install/applications/surfrace It should be pretty straightforward. Please follow the instructions and tell me if you get stuck anywhere. Greetings, Raik On Wed, Sep 4, 2013 at 2:58 AM, OOMMEN KM <oom...@gm...> wrote: > Hi, > > Please help to make my Biskit installation to use SurfaceRacer instead > WhatIf. > > Oommen Mathew > > ------------------------------------------------------------------------------ > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! > Discover the easy way to master current and previous Microsoft technologies > and advance your career. Get an incredible 1,500+ hours of step-by-step > tutorial videos with LearnDevNow. Subscribe today and save! > http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk > _______________________________________________ > Biskit-general mailing list > Bis...@li... > https://lists.sourceforge.net/lists/listinfo/biskit-general > -- ___________________________________ Raik Grünberg http://www.raiks.de/contact.html ___________________________________ |
From: OOMMEN KM <oom...@gm...> - 2013-09-05 04:13:26
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Thanks a lot Raik for the reply. I have biskit installation on Ubuntu 12.04. I am trying to use it for protein-protein docking. I doubt, I have change little part of the code in hexInput.py from scripts to use Surfaceracer. I made the following changes at line 158: rec_asa.addSurfaceRacer() at line 162: lig_asa.addSurfaceRacer() Is it correct? I am getting the following error while i run hexInput (I am following the steps given @ http://biskit.pasteur.fr/use/workflows/docking) Calculating receptor surface profile Warning (ignored): Cannot read/update profiles from source: ProfileError('Profile relMS has wrong length.',) <class 'Biskit.ProfileCollection.ProfileError'> in /home2/oommenkm/py/Biskit/PDBParseModel.py line 107: ('Profile relMS has wrong length.',). Traceback (most recent call last): File "/home2/oommenkm/py/biskit/scripts//Dock/hexInput.py", line 332, in <module> main(options) File "/home2/oommenkm/py/biskit/scripts//Dock/hexInput.py", line 179, in main rec_asa.addSurfaceRacer() File "/home2/oommenkm/py/Biskit/PDBDope.py", line 281, in addSurfaceRacer fs = SurfaceRacer( self.m, probe, vdw_set=vdw_set ) File "/home2/oommenkm/py/Biskit/SurfaceRacer.py", line 133, in __init__ self.model = model.clone() File "/home2/oommenkm/py/Biskit/PDBModel.py", line 2343, in clone return self.take( self.atomRange() ) File "/home2/oommenkm/py/Biskit/PCRModel.py", line 77, in take r = PDBModel.take( self, i, rindex=rindex, cindex=cindex ) File "/home2/oommenkm/py/Biskit/PDBModel.py", line 2266, in take r.xyz = N.take( self.getXyz(), i ) File "/usr/lib/python2.7/dist-packages/numpy/oldnumeric/functions.py", line 16, in take return np.take(a, indicies, axis) File "/usr/lib/python2.7/dist-packages/numpy/core/fromnumeric.py", line 103, in take return take(indices, axis, out, mode) IndexError: index out of range for array Please help Me. Mr. Oommen Mathew | +91 9945128780 (Karnataka) | +91 9446917322 (Kerala) On Wed, Sep 4, 2013 at 5:39 PM, Raik Grünberg <rai...@gm...>wrote: > Hi Oommen, > > whatif is not really supported by Biskit any longer. We just left the > module in place, in case people want to play around with it or update it > themselves. > > The installation of Surface Racer for Biskit is described here: > http://biskit.pasteur.fr/install/applications/surfrace > > It should be pretty straightforward. Please follow the instructions and > tell me if you get stuck anywhere. > Greetings, > Raik > > > > On Wed, Sep 4, 2013 at 2:58 AM, OOMMEN KM <oom...@gm...> wrote: > >> Hi, >> >> Please help to make my Biskit installation to use SurfaceRacer instead >> WhatIf. >> >> Oommen Mathew >> >> ------------------------------------------------------------------------------ >> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! >> Discover the easy way to master current and previous Microsoft >> technologies >> and advance your career. Get an incredible 1,500+ hours of step-by-step >> tutorial videos with LearnDevNow. Subscribe today and save! >> >> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk >> _______________________________________________ >> Biskit-general mailing list >> Bis...@li... >> https://lists.sourceforge.net/lists/listinfo/biskit-general >> > > > > -- > ___________________________________ > Raik Grünberg > http://www.raiks.de/contact.html > ___________________________________ > |
From: Raik G. <rai...@gm...> - 2013-09-06 12:51:58
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Hi Oommen, now we are talking... thanks for the report. I haven't touched the docking code in a while so I need some more time to look into it. But this doesn't seem to be docking related but the surfaceracer code is not able to make a simple copy of the input PDBModel. Usually that means something is very seriously wrong with this rec_asa model. Like, perhaps it has 0 coordinates? First question: Can you run the SurfaceRacer test case without problems? It's described on the installation page I sent you. Just run python SurfaceRacer.py If that passes, could you zip up and send me your docking project folder so that I can try reproducing the error? There could have sneaked a bug in those docking scripts because the scripts themselves are not covered by the unit tests. Best regards, Raik On Thu, Sep 5, 2013 at 12:12 AM, OOMMEN KM <oom...@gm...> wrote: > Thanks a lot Raik for the reply. > > I have biskit installation on Ubuntu 12.04. > I am trying to use it for protein-protein docking. > I doubt, I have change little part of the code in hexInput.py from scripts > to use Surfaceracer. > > I made the following changes > at line 158: rec_asa.addSurfaceRacer() > at line 162: lig_asa.addSurfaceRacer() > > Is it correct? > > > I am getting the following error while i run hexInput (I am following the > steps given @ http://biskit.pasteur.fr/use/workflows/docking) > > > Calculating receptor surface profile > Warning (ignored): Cannot read/update profiles from source: > ProfileError('Profile relMS has wrong length.',) > <class 'Biskit.ProfileCollection.ProfileError'> in > /home2/oommenkm/py/Biskit/PDBParseModel.py line 107: > ('Profile relMS has wrong length.',). > > Traceback (most recent call last): > File "/home2/oommenkm/py/biskit/scripts//Dock/hexInput.py", line 332, in > <module> > main(options) > File "/home2/oommenkm/py/biskit/scripts//Dock/hexInput.py", line 179, in > main > rec_asa.addSurfaceRacer() > File "/home2/oommenkm/py/Biskit/PDBDope.py", line 281, in addSurfaceRacer > fs = SurfaceRacer( self.m, probe, vdw_set=vdw_set ) > File "/home2/oommenkm/py/Biskit/SurfaceRacer.py", line 133, in __init__ > self.model = model.clone() > File "/home2/oommenkm/py/Biskit/PDBModel.py", line 2343, in clone > return self.take( self.atomRange() ) > File "/home2/oommenkm/py/Biskit/PCRModel.py", line 77, in take > r = PDBModel.take( self, i, rindex=rindex, cindex=cindex ) > File "/home2/oommenkm/py/Biskit/PDBModel.py", line 2266, in take > r.xyz = N.take( self.getXyz(), i ) > File "/usr/lib/python2.7/dist-packages/numpy/oldnumeric/functions.py", > line 16, in take > return np.take(a, indicies, axis) > File "/usr/lib/python2.7/dist-packages/numpy/core/fromnumeric.py", line > 103, in take > return take(indices, axis, out, mode) > IndexError: index out of range for array > > > Please help Me. > > > Mr. Oommen Mathew | +91 9945128780 (Karnataka) | +91 9446917322 (Kerala) > > > > On Wed, Sep 4, 2013 at 5:39 PM, Raik Grünberg <rai...@gm...>wrote: > >> Hi Oommen, >> >> whatif is not really supported by Biskit any longer. We just left the >> module in place, in case people want to play around with it or update it >> themselves. >> >> The installation of Surface Racer for Biskit is described here: >> http://biskit.pasteur.fr/install/applications/surfrace >> >> It should be pretty straightforward. Please follow the instructions and >> tell me if you get stuck anywhere. >> Greetings, >> Raik >> >> >> >> On Wed, Sep 4, 2013 at 2:58 AM, OOMMEN KM <oom...@gm...> wrote: >> >>> Hi, >>> >>> Please help to make my Biskit installation to use SurfaceRacer instead >>> WhatIf. >>> >>> Oommen Mathew >>> >>> ------------------------------------------------------------------------------ >>> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! >>> Discover the easy way to master current and previous Microsoft >>> technologies >>> and advance your career. Get an incredible 1,500+ hours of step-by-step >>> tutorial videos with LearnDevNow. Subscribe today and save! >>> >>> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> Biskit-general mailing list >>> Bis...@li... >>> https://lists.sourceforge.net/lists/listinfo/biskit-general >>> >> >> >> >> -- >> ___________________________________ >> Raik Grünberg >> http://www.raiks.de/contact.html >> ___________________________________ >> > > -- ___________________________________ Raik Grünberg http://www.raiks.de/contact.html ___________________________________ |