biskit-general — questions & suggestions

[Biskit-general] SurfaceRacer segmentation fault on input PDB:

[Ofer C. <ofe...@ya...>]

Dear SurfaceRacer people
SurfaceRacer works great for us, but it gives a segmentation fault in the scenario below. The input PDB was 2nxy (attached)
Can you please advise?

Many Thanks!
Ofer ChayProgrammerTel Aviv University > ./surfrace5_0_linux_64bitSurface Racer 5.0 by Oleg TsodikovAnalytical surface area calculation
Van del Waals radii sets:1 - Richards (1977)2 - Chothia  (1976)Press 1 or 2 to choose a van der Waals radius assignment:2
Input PDB file of the structure:pdb2nxy.ent
Input the probe radius in Angstroms:1.4
Enter a number to choose the calculation mode:1- Accessible surface area only2- Accessible and molecular surface areas3- Accessible, molecular surface areas and average curvature of MSMode number:2
Reading atomic coordinates and assigning radii ...1000 atoms traced2000 atoms traced3000 atoms traced4000 atoms traced5000 atoms traced6000 atoms tracedSegmentation fault

Re: [Biskit-general] How to setup biskit to use SurfaceRacer instead WhatIf

[Raik G. <rai...@gm...>]

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
___________________________________

Re: [Biskit-general] How to setup biskit to use SurfaceRacer instead WhatIf

[OOMMEN KM <oom...@gm...>]

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
> ___________________________________
>

Re: [Biskit-general] How to setup biskit to use SurfaceRacer instead WhatIf

[Raik G. <rai...@gm...>]

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
___________________________________

[Biskit-general] How to setup biskit to use SurfaceRacer instead WhatIf

[OOMMEN KM <oom...@gm...>]

Hi,

Please help to make my Biskit installation to use  SurfaceRacer instead
WhatIf.

Oommen Mathew

Re: [Biskit-general] Broken Links in Docking Example Workflow page

[Raik G. <rai...@gm...>]

Hi Paul,

thanks again for the notification. I fixed the links.

A word of warning though: I haven't myself used the docking pipeline in
several years. The individual python modules are passing their unitTests
but the Hex wrapper (Biskit/Dock/Docker.py and HexParser.py) has not been
updated to the latest version of Hex. This is a bit of a shame because the
overall infrastructure is probably still the most complete protein docking
platform with lots of features that you find anywhere else (like the
complex randomization, efficient management and filtering of millions of
docking results and several contact-based clustering methods). But you will
probably have to get your hands dirty (meaning going into the Python code)
to get everything running with the latest software.

If you want to invest some time, I can help and advise. We can also contact
the hex developer Dave Ritchie, who would probably be happy to help us with
adapting the wrapper.

Greetings
Raik

[Biskit-general] Broken Links in Docking Example Workflow page

[Paul R. <pau...@gm...>]

Hi there,

Just want to let you know that the links corresponding to "two other files
that might be worth having a closer look at are the test scripts" are not
working. I would be interested in looking at them if possible, as I am
trying to learn how to use biskit for docking.

Cheers
Paul

Re: [Biskit-general] Broken Link in Introduction to Biskit

[Raik G. <rai...@gm...>]

Hi Paul,

thanks for pointing this out. I have linked to the "Tentative Python
Tutorial" now. That's probably the best point to start. The official
Reference Manual is a bit intimidating for a beginner (but usefull later
on).

Greetings
Raik


On Thu, May 30, 2013 at 11:15 AM, Paul Reginato <pau...@gm...
> wrote:

> Hi there,
>
> I just want to let you know that on the introduction page for biskit (
> http://biskit.pasteur.fr/doc/introduction ) the link to " array
> handling chapter <
> http://numeric.scipy.org/numpydoc/numpy-9.html#pgfId-36422>"
> in section 2 "Before you start..." is broken. I'd like to check out the
> info it is supposed to link to, and I ran into the problem.
>
> Cheers
> Paul
>
> ------------------------------------------------------------------------------
> Get 100% visibility into Java/.NET code with AppDynamics Lite
> It's a free troubleshooting tool designed for production
> Get down to code-level detail for bottlenecks, with <2% overhead.
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap2
> _______________________________________________
> Biskit-general mailing list
> Bis...@li...
> https://lists.sourceforge.net/lists/listinfo/biskit-general
>



-- 
___________________________________
Raik Grünberg
http://www.raiks.de/contact.html
___________________________________

[Biskit-general] Broken Link in Introduction to Biskit

[Paul R. <pau...@gm...>]

Hi there,

I just want to let you know that on the introduction page for biskit (
http://biskit.pasteur.fr/doc/introduction ) the link to " array
handling chapter <http://numeric.scipy.org/numpydoc/numpy-9.html#pgfId-36422>"
in section 2 "Before you start..." is broken. I'd like to check out the
info it is supposed to link to, and I ran into the problem.

Cheers
Paul

Re: [Biskit-general] pdb prep for amber

[Raik G. <rai...@gm...>]

Hi Clyde,

there's indeed issues with the concat method here. So here is what
worked for me:

import Biskit as B

gfp = B.PDBModel('1GFL')
chromo = gfp.takeResidues([64,65])

del chromo.residues['biomol']   ## remove the bioUnit residue profile

parm = B.AmberParmBuilder( chromo )
chromo = parm.capNME( chromo, 0 )
chromo = parm.capACE( chromo, 0 )

Don't ask. Because of the chain breaking bug, the order of the two
calls matters.

You are right, there is another version in PDBCleaner already. That's
the one to be used actually.
Anyway, I have checked in bug fixes of the underlying chain break
issue (for ParmBuilder, not the PDBCleaner yet). So, if you svn update
your Biskit project. It should work. Didn't have much time for proper
testing though.

If all fails, you should be able to do this by hand:

del chromo.residues['biomol']   ## remove the bioUnit residue profile

m1 = parm.capACE( chromo, 0 )
m2 = parm.capNME( chromo, 0 )  ## separately always worked for me

m_result = m1.concat( m2.takeResidues( [-1] ), newChain=False )

And then cross fingers etc...

Got to run now, I hope I find the time this week to prepare a proper
fix for the deeper issue.

Greetings and Good luck!
Raik

On Tue, Apr 23, 2013 at 11:20 AM, Clyde Fare <cly...@gm...> wrote:
> Hey Raik,
>
> Thanks for the info, I have problems if I pass in a model with a single
> chain to the method, the final concat call when capACE returns get's called
> on an empty model and this leads to a 'ValueError: max() arg is an empty
> sequence' in PDBModel.py.
>
> btw. I notice there is a slightly different version of the capping functions
> in PDBCleaner. From my brief skim they appear pretty similar and both give
> the above error.
>
> I'll have a play with it and if I get anywhere I'll let you knew.
>
> Thanks for the advice.
>
> Cheers
>
> Clyde
>
>
> On 23 April 2013 15:10, Raik Grünberg <rai...@gm...> wrote:
>>
>> Actually, hold on, there is still something going wrong even with my
>> workaround.
>>
>> On Tue, Apr 23, 2013 at 10:08 AM, Raik Grünberg
>> <rai...@gm...> wrote:
>> > Hi Clyde,
>> >
>> > you are on the right track. One small fix that you probably have
>> > already found is that capNME and capACE return the capped model rather
>> > than modifying the internal model of ParmBuilder. So you have to
>> > capture their return value. (I guess those two methods should really
>> > go somewhere else like into the PDBCleaner)
>> >
>> > However, if you got this far, I guess what you are getting is this:
>> > Biskit.ProfileCollection.ProfileError: Can't take sub-profile
>> > 'biomol': IndexError('index out of range for array',)
>> >
>> > This is a bug. I am working on it. capNME and capACE use
>> > PDBModel.concat to append the NME or ACE residue. And, for some
>> > reason, this concat is messing up the residue profile 'biomol' which
>> > contains the biological unit info. Here is a work-around until I fix
>> > it:
>> >
>> > import Biskit as B
>> >
>> > gfp = B.PDBModel('1GFL')
>> > chromo = gfp.takeResidues([64,65])
>> >
>> > del chromo.residues['biomol']   ## remove the bioUnit residue profile
>> >
>> > parm = B.AmberParmBuilder( chromo )
>> > m = parm.capACE( chromo, 0 )
>> > m = parm.capNME( m, 0 )
>> >
>> > Note that I am passing the result of capACE into capNME and then
>> > capture the result of that. You can also just pass around chromo.
>> >
>> > Good luck!
>> > Raik
>> >
>> >
>> > On Tue, Apr 23, 2013 at 7:57 AM, Clyde Fare <cly...@gm...>
>> > wrote:
>> >> Hello,
>> >>
>> >> I'm a PHD student starting some QM:MM calculations and I'm just getting
>> >> used to Biskit. It's an amazing library - thanks for all the hard work
>> >> you
>> >> guys must have put in. :). I'm still a little fuzzy on how to best use
>> >> it,
>> >> in particular I would like to prepare raw pdb files for an amber
>> >> molecular
>> >> mechanics calculation and I was wondering whether I could get a little
>> >> guidance.
>> >>
>> >> Having looked at your amber-sampling tutorial I think I can automate
>> >> much
>> >> of the cleaning phase but I'm looking at GFP and it has non standard
>> >> residues that need parameterisation. I'm trying to consturct an
>> >> automated
>> >> way of parameterising these residues. I had a look at the
>> >> AmberParmBuilder
>> >> class but it looks like the parmMirror method is not suitable for this
>> >> usage - is there an obvious approach for attempting this using Biskit?
>> >>
>> >> I'm thinking of extracting the nonstandard residues capping the N and C
>> >> ends and then using antechamber on the subsequent pdb file, however
>> >> when I
>> >> try and use the capNME and capACE methods I get an error if I only have
>> >> a
>> >> single chain (see below for code I'm using), have I misunderstood what
>> >> these methods do/ can you point me in the right direction for how to do
>> >> this?
>> >>
>> >> Cheers
>> >>
>> >> Clyde
>> >>
>> >>
>> >> import Biskit
>> >> gfp_raw=Biskit.PDBModel('1GFL.pdb')
>> >> non_standard = gfp_raw.takeResidues([64,65])
>> >>
>> >> parm_build.capNME(non_standard,0)
>> >> parm_build.capACE(non_standard,0)
>> >>
>> >> #get_connectivity(non_standard)
>> >> #get_atom_types(non_standard)
>> >> #get_partial_charges(non_standard)
>> >>
>> >> ------------------------------------------------------------------------------
>> >> Try New Relic Now & We'll Send You this Cool Shirt
>> >> New Relic is the only SaaS-based application performance monitoring
>> >> service
>> >> that delivers powerful full stack analytics. Optimize and monitor your
>> >> browser, app, & servers with just a few lines of code. Try New Relic
>> >> and get this awesome Nerd Life shirt!
>> >> http://p.sf.net/sfu/newrelic_d2d_apr
>> >> _______________________________________________
>> >> 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
>> ___________________________________
>
>



-- 
___________________________________
Raik Grünberg
http://www.raiks.de/contact.html
___________________________________

Re: [Biskit-general] pdb prep for amber

[Raik G. <rai...@gm...>]

Hi Clyde,

you are on the right track. One small fix that you probably have
already found is that capNME and capACE return the capped model rather
than modifying the internal model of ParmBuilder. So you have to
capture their return value. (I guess those two methods should really
go somewhere else like into the PDBCleaner)

However, if you got this far, I guess what you are getting is this:
Biskit.ProfileCollection.ProfileError: Can't take sub-profile
'biomol': IndexError('index out of range for array',)

This is a bug. I am working on it. capNME and capACE use
PDBModel.concat to append the NME or ACE residue. And, for some
reason, this concat is messing up the residue profile 'biomol' which
contains the biological unit info. Here is a work-around until I fix
it:

import Biskit as B

gfp = B.PDBModel('1GFL')
chromo = gfp.takeResidues([64,65])

del chromo.residues['biomol']   ## remove the bioUnit residue profile

parm = B.AmberParmBuilder( chromo )
m = parm.capACE( chromo, 0 )
m = parm.capNME( m, 0 )

Note that I am passing the result of capACE into capNME and then
capture the result of that. You can also just pass around chromo.

Good luck!
Raik


On Tue, Apr 23, 2013 at 7:57 AM, Clyde Fare <cly...@gm...> wrote:
> Hello,
>
> I'm a PHD student starting some QM:MM calculations and I'm just getting
> used to Biskit. It's an amazing library - thanks for all the hard work you
> guys must have put in. :). I'm still a little fuzzy on how to best use it,
> in particular I would like to prepare raw pdb files for an amber molecular
> mechanics calculation and I was wondering whether I could get a little
> guidance.
>
> Having looked at your amber-sampling tutorial I think I can automate much
> of the cleaning phase but I'm looking at GFP and it has non standard
> residues that need parameterisation. I'm trying to consturct an automated
> way of parameterising these residues. I had a look at the AmberParmBuilder
> class but it looks like the parmMirror method is not suitable for this
> usage - is there an obvious approach for attempting this using Biskit?
>
> I'm thinking of extracting the nonstandard residues capping the N and C
> ends and then using antechamber on the subsequent pdb file, however when I
> try and use the capNME and capACE methods I get an error if I only have a
> single chain (see below for code I'm using), have I misunderstood what
> these methods do/ can you point me in the right direction for how to do
> this?
>
> Cheers
>
> Clyde
>
>
> import Biskit
> gfp_raw=Biskit.PDBModel('1GFL.pdb')
> non_standard = gfp_raw.takeResidues([64,65])
>
> parm_build.capNME(non_standard,0)
> parm_build.capACE(non_standard,0)
>
> #get_connectivity(non_standard)
> #get_atom_types(non_standard)
> #get_partial_charges(non_standard)
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
> New Relic is the only SaaS-based application performance monitoring service
> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
> _______________________________________________
> Biskit-general mailing list
> Bis...@li...
> https://lists.sourceforge.net/lists/listinfo/biskit-general



-- 
___________________________________
Raik Grünberg
http://www.raiks.de/contact.html
___________________________________

[Biskit-general] pdb prep for amber

[Clyde F. <cly...@gm...>]

Hello,

I'm a PHD student starting some QM:MM calculations and I'm just getting
used to Biskit. It's an amazing library - thanks for all the hard work you
guys must have put in. :). I'm still a little fuzzy on how to best use it,
in particular I would like to prepare raw pdb files for an amber molecular
mechanics calculation and I was wondering whether I could get a little
guidance.

Having looked at your amber-sampling tutorial I think I can automate much
of the cleaning phase but I'm looking at GFP and it has non standard
residues that need parameterisation. I'm trying to consturct an automated
way of parameterising these residues. I had a look at the AmberParmBuilder
class but it looks like the parmMirror method is not suitable for this
usage - is there an obvious approach for attempting this using Biskit?

I'm thinking of extracting the nonstandard residues capping the N and C
ends and then using antechamber on the subsequent pdb file, however when I
try and use the capNME and capACE methods I get an error if I only have a
single chain (see below for code I'm using), have I misunderstood what
these methods do/ can you point me in the right direction for how to do
this?

Cheers

Clyde


import Biskit
gfp_raw=Biskit.PDBModel('1GFL.pdb')
non_standard = gfp_raw.takeResidues([64,65])

parm_build.capNME(non_standard,0)
parm_build.capACE(non_standard,0)

#get_connectivity(non_standard)
#get_atom_types(non_standard)
#get_partial_charges(non_standard)

Re: [Biskit-general] Generation of protein conformers using BISKIT

[Raik G. <rai...@cr...>]

Hi Horacio,

actually, for this problem, Biskit doesn't have a ready-made solution.
The Biskit PDBModel is array-based. There is no built-in topology or
connectivity information. So we don't have functions to turn around a
certain bond. What you would have to do is something like this:

1) load PDB

import Biskit as B
m = B.PDBModel('your_file.pdb')

2) split the PDBModel into two, right at the bond you want to turn.
E.g. if your bond is between atom 500 and atom 501 (first atom is 0)
then:

m1 = m.take( range(0,501) )   ## all from 0 .. (including) 500
m2 = m.take( range(501, len(m) ) ) ## all from 501 ... end

3) Now you have to calculate your rotation matrix yourself, sorry,
can't help you with that. The coordinates of the first atom of m2 are:

origin = m2.xyz[0]

rotation = zeros( 3,3 )
.... now calculate your rotation matrix ...

translation = numpy.array( [0.0, 0.0, 0.0])  # no translation

4) apply the rotation to second half of the PDB:

m2 = m2.transform( rotation, translation )


5) join the two models back together

mfinal = m1.concat( m2 )
mfinal.writePdb( 'your_result.pdb')

Actually, you can probably make things easier by centering your
coordinates on the first atom after the bond (in step 1)

m.xyz = m.xyz - m.xyz[501]
If I am not messing this up, this should translate the coordinates
such that atom 501 is (0,0,0)
You still have to figure out how to create your rotation matrix. I am
not mathematician enough for that. The nice thing is though that once
you have a rotation matrix for a turn by 1 degree, you can just apply
the same matrix in a loop 360 times.

So yes, that's about as good as it gets with Biskit. UCSF Chimera has
some model building options and is also python based. Perhaps you can
find ready-to-go solution there. I didn't test the code I wrote up
there, there might be typos or errors. Ah, and if you come up with a
general solution, don't hesitate to send me your modification and I am
happy to add a new method to PDBModel :-)

Good luck!
Greetings from Montreal,
Raik



On Mon, Mar 11, 2013 at 4:17 PM, Horacio Pérez-Sánchez <ho...@um...> wrote:
> Good morning,
>
> I have recently read about BISKIT. For some publication that we have ready
> to submit we need to add some calculations; for some PDB structures we need
> to focus on a concrete dihedral angle and generate all conformations
> (different pdb files for each new value of the angle) when we change that
> angle by increments. I wonder where could I find just this exact information
> (I do not need anything else), or if there is a tutorial that explains this
> part.
>
> Thanks,
> Horacio
>
> ==============================================
> Horacio Pérez-Sánchez, PhD
> Parallel Computer Architecture Group: http://www.um.es/gacop
> School of Computer Science, University of Murcia (Spain)
> Email: ho...@um...
> Tel: + 34 868 88 8509
> ==============================================
>
>
>
>



-- 
--
___________________________________
Raik Grünberg
http://www.raiks.de/contact.html
___________________________________

Re: [Biskit-general] align.py error

[Raik G. <rai...@gm...>]

For the record, I have opened a bug report for this: bug ID 3530850
https://sourceforge.net/tracker/?func=detail&aid=3530850&group_id=150896&atid=779191

Greetings,
Raik

On Wed, May 30, 2012 at 9:52 AM, Raik Grünberg <rai...@gm...> wrote:
>> More specifically, something goes
>>
>
> The cut & paste got garbled up. What I meant to say is that something
> goes wrong in the parsing (type-casting) of the [BINARY] section of
> the file.
>
> Greetings
> Raik
>
>> If you haven't modified anything there, please insert the following
>> debugging code into the file Biskit/ExeConfig.py starting at line 193:
>>
>>                ## leave default value if None is given
>>                try:
>>                    if value is not '':
>>                        self.__dict__[ key ] = t( value )
>>                except TypeError, what:
>>                    report = {}
>>                    report['key'] = key
>>                    report['value'] = value
>>                    report['dconf'] = dconf
>>                    report['t'] = t
>>                    T.dump( 'report_ExeConfig.dat' )
>>                    raise TyperError, what
>>
>> This will not fix the error but it will create a little report
>> dictionary and dump it into a file 'report_ExeConfig.dat' inside your
>> current directory. If you could send me this file, that should be
>> enough to sort out what's going wrong here.
>>
>> Actually, I am attaching the modified ExeConfig.py, rename the
>> original (don't override!) and replace it by the one attached.
>> Untested but it should work.
>>
>> I hope that helps,
>> Raik
>>
>> On Wed, May 30, 2012 at 7:06 AM, Roberto Togawa
>> <rob...@em...> wrote:
>>> Hi,
>>>
>>> I'm running the homology modelling pipeline. I'm testing the scripts, because I'm changing the machine that Biskit was installed before.
>>> All the previous steps (search_sequences.py, search_templates.py, clean_templates.py, setup_validation.py), runs fine, but when I ran align.py, it come up with the error at the end of this e-mail.
>>> Any clue about this error. Do I missing any program that should be installed?
>>> I have no problem executing t_coffee in the Linux prompt.
>>> Cheers,
>>> Roberto
>>>
>>> togawa@proteinmodelling-server:/temp/test$ /usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py
>>>
>>> Warning (ignored): Could not import PVM (Parallel Virtual Machine) modules. Please check that PVM and pypvm are installed!
>>> Parallelisation is not available.
>>>
>>> Error: Error while building alingnments.
>>> <type 'exceptions.TypeError'> in /usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py line 123:
>>> ("cannot create 'NoneType' instances",).
>>> TraceBack:
>>> align: 123 (<module>) a.align_for_modeller_inp()
>>> Aligner: 273 (align_for_modeller_inp) fasta_sequences, fasta_target )
>>> Aligner: 227 (__default_input_files) cwd = TCoffee( '' ).cwd or os.getcwd()
>>> Aligner: 56 (__init__) node=host, **kw )
>>> Executor: 315 (__init__) self.exe = ExeConfigCache.get( name, strict=strict )
>>> ExeConfigCache: 68 (get) ExeConfigCache.CACHE[ name ] = ExeConfig( name, **kw )
>>> ExeConfig: 157 (__init__) self.update()
>>> ExeConfig: 194 (update) self.__dict__[ key ] = t( value )
>>>
>>>
>>> Traceback (most recent call last):
>>> File "/usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py", line 128, in <module>
>>> EHandler.error( 'Error while building alingnments.')
>>> File "/usr/lib/python2.7/dist-packages/Biskit/ErrorHandler.py", line 77, in error
>>> raise NormalError
>>> Biskit.Errors.NormalError
>>>
>>>
>>> --
>>>
>>> Roberto Togawa
>>>
>>> rob...@em...
>>>
>>> Embrapa Recursos Genéticos e Biotecnologia
>>> Laboratório de Bioinformática
>>> Parque Estação Biológica - Final W5 norte
>>> Caixa Postal 02372
>>> Brasília DF - Brasil - 70770-900
>>> Fone: +55 61 3448-4741 / fax : +55 61 3340-3658
>>>
>>> ---
>>> ------------------------------------------------------------------------------
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond. Discussions
>>> will include endpoint security, mobile security and the latest in malware
>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>> _______________________________________________
>>> 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
> ___________________________________



-- 
___________________________________
Raik Grünberg
http://www.raiks.de/contact.html
___________________________________

Re: [Biskit-general] align.py error

[Raik G. <rai...@gm...>]

> More specifically, something goes
>

The cut & paste got garbled up. What I meant to say is that something
goes wrong in the parsing (type-casting) of the [BINARY] section of
the file.

Greetings
Raik

> If you haven't modified anything there, please insert the following
> debugging code into the file Biskit/ExeConfig.py starting at line 193:
>
>                ## leave default value if None is given
>                try:
>                    if value is not '':
>                        self.__dict__[ key ] = t( value )
>                except TypeError, what:
>                    report = {}
>                    report['key'] = key
>                    report['value'] = value
>                    report['dconf'] = dconf
>                    report['t'] = t
>                    T.dump( 'report_ExeConfig.dat' )
>                    raise TyperError, what
>
> This will not fix the error but it will create a little report
> dictionary and dump it into a file 'report_ExeConfig.dat' inside your
> current directory. If you could send me this file, that should be
> enough to sort out what's going wrong here.
>
> Actually, I am attaching the modified ExeConfig.py, rename the
> original (don't override!) and replace it by the one attached.
> Untested but it should work.
>
> I hope that helps,
> Raik
>
> On Wed, May 30, 2012 at 7:06 AM, Roberto Togawa
> <rob...@em...> wrote:
>> Hi,
>>
>> I'm running the homology modelling pipeline. I'm testing the scripts, because I'm changing the machine that Biskit was installed before.
>> All the previous steps (search_sequences.py, search_templates.py, clean_templates.py, setup_validation.py), runs fine, but when I ran align.py, it come up with the error at the end of this e-mail.
>> Any clue about this error. Do I missing any program that should be installed?
>> I have no problem executing t_coffee in the Linux prompt.
>> Cheers,
>> Roberto
>>
>> togawa@proteinmodelling-server:/temp/test$ /usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py
>>
>> Warning (ignored): Could not import PVM (Parallel Virtual Machine) modules. Please check that PVM and pypvm are installed!
>> Parallelisation is not available.
>>
>> Error: Error while building alingnments.
>> <type 'exceptions.TypeError'> in /usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py line 123:
>> ("cannot create 'NoneType' instances",).
>> TraceBack:
>> align: 123 (<module>) a.align_for_modeller_inp()
>> Aligner: 273 (align_for_modeller_inp) fasta_sequences, fasta_target )
>> Aligner: 227 (__default_input_files) cwd = TCoffee( '' ).cwd or os.getcwd()
>> Aligner: 56 (__init__) node=host, **kw )
>> Executor: 315 (__init__) self.exe = ExeConfigCache.get( name, strict=strict )
>> ExeConfigCache: 68 (get) ExeConfigCache.CACHE[ name ] = ExeConfig( name, **kw )
>> ExeConfig: 157 (__init__) self.update()
>> ExeConfig: 194 (update) self.__dict__[ key ] = t( value )
>>
>>
>> Traceback (most recent call last):
>> File "/usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py", line 128, in <module>
>> EHandler.error( 'Error while building alingnments.')
>> File "/usr/lib/python2.7/dist-packages/Biskit/ErrorHandler.py", line 77, in error
>> raise NormalError
>> Biskit.Errors.NormalError
>>
>>
>> --
>>
>> Roberto Togawa
>>
>> rob...@em...
>>
>> Embrapa Recursos Genéticos e Biotecnologia
>> Laboratório de Bioinformática
>> Parque Estação Biológica - Final W5 norte
>> Caixa Postal 02372
>> Brasília DF - Brasil - 70770-900
>> Fone: +55 61 3448-4741 / fax : +55 61 3340-3658
>>
>> ---
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> 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
___________________________________

Re: [Biskit-general] align.py error

[Raik G. <rai...@gm...>]

Hi Roberto,

this one I haven't seen yet. The error occurs in the code that is
parsing your exe_t_coffee.dat configuration file. The original version
of this file is in biskit/Biskit/data/defaults. You may have created a
custom version in ~/.biskit/ in this case, this version is used. Could
you please send me your exe_t_coffee.dat file from  ~/.biskit (if any)
and from Biskit/data/defaults?

More specifically, something goes

If you haven't modified anything there, please insert the following
debugging code into the file Biskit/ExeConfig.py starting at line 193:

                ## leave default value if None is given
                try:
                    if value is not '':
                        self.__dict__[ key ] = t( value )
                except TypeError, what:
                    report = {}
                    report['key'] = key
                    report['value'] = value
                    report['dconf'] = dconf
                    report['t'] = t
                    T.dump( 'report_ExeConfig.dat' )
                    raise TyperError, what

This will not fix the error but it will create a little report
dictionary and dump it into a file 'report_ExeConfig.dat' inside your
current directory. If you could send me this file, that should be
enough to sort out what's going wrong here.

Actually, I am attaching the modified ExeConfig.py, rename the
original (don't override!) and replace it by the one attached.
Untested but it should work.

I hope that helps,
Raik

On Wed, May 30, 2012 at 7:06 AM, Roberto Togawa
<rob...@em...> wrote:
> Hi,
>
> I'm running the homology modelling pipeline. I'm testing the scripts, because I'm changing the machine that Biskit was installed before.
> All the previous steps (search_sequences.py, search_templates.py, clean_templates.py, setup_validation.py), runs fine, but when I ran align.py, it come up with the error at the end of this e-mail.
> Any clue about this error. Do I missing any program that should be installed?
> I have no problem executing t_coffee in the Linux prompt.
> Cheers,
> Roberto
>
> togawa@proteinmodelling-server:/temp/test$ /usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py
>
> Warning (ignored): Could not import PVM (Parallel Virtual Machine) modules. Please check that PVM and pypvm are installed!
> Parallelisation is not available.
>
> Error: Error while building alingnments.
> <type 'exceptions.TypeError'> in /usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py line 123:
> ("cannot create 'NoneType' instances",).
> TraceBack:
> align: 123 (<module>) a.align_for_modeller_inp()
> Aligner: 273 (align_for_modeller_inp) fasta_sequences, fasta_target )
> Aligner: 227 (__default_input_files) cwd = TCoffee( '' ).cwd or os.getcwd()
> Aligner: 56 (__init__) node=host, **kw )
> Executor: 315 (__init__) self.exe = ExeConfigCache.get( name, strict=strict )
> ExeConfigCache: 68 (get) ExeConfigCache.CACHE[ name ] = ExeConfig( name, **kw )
> ExeConfig: 157 (__init__) self.update()
> ExeConfig: 194 (update) self.__dict__[ key ] = t( value )
>
>
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py", line 128, in <module>
> EHandler.error( 'Error while building alingnments.')
> File "/usr/lib/python2.7/dist-packages/Biskit/ErrorHandler.py", line 77, in error
> raise NormalError
> Biskit.Errors.NormalError
>
>
> --
>
> Roberto Togawa
>
> rob...@em...
>
> Embrapa Recursos Genéticos e Biotecnologia
> Laboratório de Bioinformática
> Parque Estação Biológica - Final W5 norte
> Caixa Postal 02372
> Brasília DF - Brasil - 70770-900
> Fone: +55 61 3448-4741 / fax : +55 61 3340-3658
>
> ---
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Biskit-general mailing list
> Bis...@li...
> https://lists.sourceforge.net/lists/listinfo/biskit-general



-- 
___________________________________
Raik Grünberg
http://www.raiks.de/contact.html
___________________________________

[Biskit-general] align.py error

[Roberto T. <rob...@em...>]

Hi, 

I'm running the homology modelling pipeline. I'm testing the scripts, because I'm changing the machine that Biskit was installed before. 
All the previous steps (search_sequences.py, search_templates.py, clean_templates.py, setup_validation.py), runs fine, but when I ran align.py, it come up with the error at the end of this e-mail. 
Any clue about this error. Do I missing any program that should be installed? 
I have no problem executing t_coffee in the Linux prompt. 
Cheers, 
Roberto 

togawa@proteinmodelling-server:/temp/test$ /usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py 

Warning (ignored): Could not import PVM (Parallel Virtual Machine) modules. Please check that PVM and pypvm are installed! 
Parallelisation is not available. 

Error: Error while building alingnments. 
<type 'exceptions.TypeError'> in /usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py line 123: 
("cannot create 'NoneType' instances",). 
TraceBack: 
align: 123 (<module>) a.align_for_modeller_inp() 
Aligner: 273 (align_for_modeller_inp) fasta_sequences, fasta_target ) 
Aligner: 227 (__default_input_files) cwd = TCoffee( '' ).cwd or os.getcwd() 
Aligner: 56 (__init__) node=host, **kw ) 
Executor: 315 (__init__) self.exe = ExeConfigCache.get( name, strict=strict ) 
ExeConfigCache: 68 (get) ExeConfigCache.CACHE[ name ] = ExeConfig( name, **kw ) 
ExeConfig: 157 (__init__) self.update() 
ExeConfig: 194 (update) self.__dict__[ key ] = t( value ) 


Traceback (most recent call last): 
File "/usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py", line 128, in <module> 
EHandler.error( 'Error while building alingnments.') 
File "/usr/lib/python2.7/dist-packages/Biskit/ErrorHandler.py", line 77, in error 
raise NormalError 
Biskit.Errors.NormalError 


-- 

Roberto Togawa 

rob...@em... 

Embrapa Recursos Genéticos e Biotecnologia 
Laboratório de Bioinformática 
Parque Estação Biológica - Final W5 norte 
Caixa Postal 02372 
Brasília DF - Brasil - 70770-900 
Fone: +55 61 3448-4741 / fax : +55 61 3340-3658 

--- 

Re: [Biskit-general] Problem in Installing Biskit

[Asma T. <asm...@gm...>]

Hi Raik,

I will be pleased to provide you details of installation. The system
information is Windows 7 SP 1. 64 - bit operating system.

The installation path is as below:

1) On the website, it is recommended to use python 2.5 (I installed python
2.5 but numpy and scientific were not able to install even though both
modules are for python 2.5), so instead of 2.5, I installed python 2.7 and
that's why I installed numpy and scientific python for python 2.7. I am
attaching both .exe files for your reference.

*Note: Numpy, Scientifc Python and Biskit are installed in the path given
below:*
*
*
*C:\......\Python27\Lib\site-packages\*
*
*
*The details are available in the file of site.py in python folder.*

2) After installing numpy and scientific python (No error messages), I
installed Biskit (again on python 2.7). It was installed successfully.
(except those errors of biggles and PVM).

3) I downloaded the trunk folder and copied it in the Biskit folder (still
exploring)

4) On the other hand, bio-python was also installed.

5) When all three modules will be installed, the files winins and remove
application can be seen in Python 2.7 folder.

I am using Biskit, numpy and scientific python through GUI for python 2.7.

Biskit had a folder named testdata which have an example of Modelling and
docking but, as for now, I am still working on my data, exploring Biskit
and trying to have my desired results :)

Hopefully it will help other users and will fulfill your question to an
extent. I will inform you as soon as I will get success.

I didn't receive your email on 7th Jan (on which you have replied) and
until that time I have already found sequencesearcher.py and started to
have fun with it. I just received your email on Jan, 10th.

Just let me know about the Biskit online forum for users (whenever it is
created). I would love to have interaction with other users in this regard.

Thank You so much for your support and Happy New Year to you and to Biskit
:)

Best Regards,
Asma Ishaq Tahir


On Mon, Jan 9, 2012 at 9:38 PM, Raik Gruenberg <rai...@cr...>wrote:

> Hi Asma,
>
> I am copying in the biskit-general mailing list. I hope that's fine
> with you. Biskit should probably switch to some other forum at some
> point. The sourceforge mailing lists are not the most thrilling to
> use.
>
> Really glad to hear that you got the whole homology modeling pipeline
> installed on Windows. I am even a little surprised because we never
> developed for that platform and there is lots of calling from external
> programs involved. Could you do me a favor? Could you send me a very
> short summary of how you managed to install everything? Which Windows
> are you working on and what where the main stumbling blocks? I would
> put that up on the biskit web site (with your name of course) to help
> other users.
>
> On Sat, Jan 7, 2012 at 2:57 AM, Asma Tahir <asm...@gm...> wrote:
> > Hi Raik,
> >
> > BINGO! Thank you so much for your full support! It is fully installed.
> >
> > Just a question, as it is mentioned in the syntax:
> >
> > search_sequences.py [-q |target.fasta| -o |outFolder| -log |logFile| -db
> > |database| -e |e-value-cutoff| -aln |n_alignments| -psi]
> >
> > about database, how can we direct them to the online database? like
> > SwissProt etc or NCBI? or we have to create manually the database?
>
> We have a method in Biskit/Mod/SequenceSearcher that implements remote
> blast searches (via BioPython). There are two test cases for this
> method in the python module and last time I tested it, it still worked
> fine. However, we never included this remote option in the general
> modeling work flow. The problem is that we still need the local
> database for fetching the actual sequence record. Currently
> SequenceSearcher uses the local 'fastacmd' program for that. We never
> implemented a remote alternative for this function. It shouldn't be
> very difficult though.
>
> The important code to look at is def fastaRecordFromId( self, db, id )
> within SequenceSearcher.py. So you would basically need to write an
> alternative method that takes the same input but uses the online
> databases. I guess BioPython meanwhile should have some methods in
> that direction.
>
> If you manage, please tell me and we can quickly work this function
> back into the pipeline. I am not sure when I will fnd the time to do
> it myself...
>
> Thanks and Good Luck (and Happy New Year!),
> Raik
>
> >
> > Please let me know also about any online forum or blog related to Biskit
> > release and Q/A.
> >
> > Thanks once again!
> >
> > Best Regards,
> >
> > Asma Ishaq Tahir
> > Research Technical Assistant
> >
> > On Wed, Jan 4, 2012 at 5:12 PM, Raik Gruenberg <rai...@cr...>
> > wrote:
> >>
> >> Hi Amir,
> >>
> >> that looks good then! Don't worry too much about the PVM error
> >> message. It will be rather difficult to get PVM installed on a windows
> >> system anyway. It can already be quite painful even on Linux. If you
> >> are annoyed by it, simply edit Biskit/PVM/__init__.py and switch off
> >> the message by commenting out:
> >>
> >> if not pvm_installed:
> >>    EHandler.warning('Could not import PVM (Parallel Virtual Machine)
> >> modules.'+
> >>        ' Please check that PVM and pypvm are installed!\n'+
> >>        '\tParallelisation is not available.')
> >>
> >> Biskit also works very well without Biggles but several modules use
> >> Biggles for making nice plots so it would be nice to get it running.
> >> The basic idea is to install the plotutils library and then you need
> >> to compile the biggles library against that. This compilation is
> >> automatted in the typical
> >> python setup.py build
> >> step but it requires compilation tools, like a C-compiler.
> >>
> >> I have honestly no idea how that works on Windows... If you don't
> >> manage to get Biggles running, there is also good plotting methods
> >> included in the SciPy package. SciPy surely comes with ready-made
> >> windows installers. Just that you will then have to create all your
> >> plots from scratch and cannot use the ones that are already built-into
> >> Biskit.
> >>
> >> For very quick and dirty plotting, gnuplot is very useful and is used
> >> by some Biskit methods too. So if you just install gnuplot (described
> >> in the windows install section on biskit.fr) you will already be able
> >> to quickly make some simple scatter,  line plots and histograms.
> >> That's actually what I am using most of the time.
> >>
> >> Hope that helps,
> >> Raik
> >>
> >> On Wed, Jan 4, 2012 at 1:09 AM, Asma Tahir <asm...@gm...>
> wrote:
> >> > Hi Raik,
> >> >
> >> > Thank you so much for your reply!
> >> >
> >> > Yup, I am using Windows. Your recommendations helped me a lot but now
> I
> >> > got
> >> > stuck at the end.... (I have added the trunk folder in
> >> > C:\Python27\lib\site-packages\Biskit)
> >> >
> >> > When I type import Biskit in python, it will give me following error
> >> > message:
> >> >
> >> > Warning: Could not import PVM (Parallel Virtual Machine) modules.
> Please
> >> > check that pvm and pypvm are installed.
> >> > Warning: Could not import biggles module. Plotting is not available.
> >> >
> >> > Biggles and PVM is already in the Trunk folder (The one I put in
> Biskit
> >> > folder).
> >> >
> >> > For the other two commands (for numpy and Scientific), no error
> message
> >> > at
> >> > all.
> >> >
> >> > Please advice.
> >> >
> >> > Thank You and Best Regards,
> >> >
> >> > Asma Ishaq Tahir
> >> > Research Technical Assistant
> >> >
> >> > On Wed, Jan 4, 2012 at 5:44 AM, Raik Gruenberg <rai...@cr...
> >
> >> > wrote:
> >> >>
> >> >> Hi Asma,
> >> >>
> >> >> you are trying a Windows installation, right? I haven't tested that
> in
> >> >> a very long time. In any case, the current installation packages on
> >> >> sourceforge are rather out of date. I have started working on a new
> >> >> release but hadn't the time yet to finish it.
> >> >>
> >> >> On Windows, your best bet for the moment is to install things
> manually:
> >> >> 1) python
> >> >> 2) numpy
> >> >> 3) scientific python
> >> >> As briefly described on
> >> >> http://biskit.pasteur.fr/install/windows_install/ but you should of
> >> >> course use more recent versions of everything.
> >> >>
> >> >> Make sure that numpy and Scientific Python can be used from the
> python
> >> >> you installed. E.g. open an a python interpreter and enter:
> >> >>
> >> >> import numpy
> >> >> import Scientific
> >> >>
> >> >> Both should run through without error messages.
> >> >>
> >> >> Then use SVN to retrieve the current development snapshot of biskit.
> >> >> There are also some graphical tools. Or you download and unpack the
> >> >> daily source tarball from Sourceforge:
> >> >> http://biskit.svn.sourceforge.net/viewvc/biskit/trunk/?view=tar
> >> >>
> >> >> Unpack the content of this archive file into a folder named
> >> >> 'biskitproject' or similar. And then add the folder
> >> >> C:\....biskitproject/Biskit to your PYTHONPATH.
> >> >>
> >> >> python
> >> >> import Biskit
> >> >>
> >> >> should then work (the first time, you will receive messages about
> >> >> config files that are being created).
> >> >>
> >> >>
> >> >> One note of caution -- Biskit on Windows is rather untested
> territory.
> >> >> I suspect that many of the third-party software wrappers will
> probably
> >> >> not work.
> >> >>
> >> >> I hope this is helping somewhat. Please tell me if you get it
> running.
> >> >> Perhaps you could then help to update the installation section on the
> >> >> web site.
> >> >>
> >> >> Greetings,
> >> >> Raik
> >> >>
> >> >>
> >> >> On Tue, Jan 3, 2012 at 2:26 AM, Asma Tahir <asm...@gm...>
> >> >> wrote:
> >> >> > Greetings!
> >> >> >
> >> >> > I encountered problem in installing biskit. I have already
> installed
> >> >> > python
> >> >> > 2.5 but numpy is unable to found the python 2.5 in registry. I also
> >> >> > have
> >> >> > python 2.7. Biskit.exe can recognize only python 2.7 but not python
> >> >> > 2.5.
> >> >> >
> >> >> > Kindly advice.
> >> >> >
> >> >> > Thank you and Best Regards,
> >> >> >
> >> >> >
> >> >> > *Asma Ishaq Tahir*
> >> >> > *Research Technical Assistant*
> >> >> >
> >> >> >
> >> >> >
> ------------------------------------------------------------------------------
> >> >> > Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a
> >> >> > complex
> >> >> > infrastructure or vast IT resources to deliver seamless, secure
> >> >> > access
> >> >> > to
> >> >> > virtual desktops. With this all-in-one solution, easily deploy
> >> >> > virtual
> >> >> > desktops for less than the cost of PCs and save 60% on VDI
> >> >> > infrastructure
> >> >> > costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
> >> >> > _______________________________________________
> >> >> > 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
> >> ___________________________________
> >
> >
>
>
>
> --
> --
> ___________________________________
> Raik Grünberg
> http://www.raiks.de/contact.html
> ___________________________________
>

Re: [Biskit-general] Problem in Installing Biskit

[Raik G. <rai...@cr...>]

Hi Asma,

I am copying in the biskit-general mailing list. I hope that's fine
with you. Biskit should probably switch to some other forum at some
point. The sourceforge mailing lists are not the most thrilling to
use.

Really glad to hear that you got the whole homology modeling pipeline
installed on Windows. I am even a little surprised because we never
developed for that platform and there is lots of calling from external
programs involved. Could you do me a favor? Could you send me a very
short summary of how you managed to install everything? Which Windows
are you working on and what where the main stumbling blocks? I would
put that up on the biskit web site (with your name of course) to help
other users.

On Sat, Jan 7, 2012 at 2:57 AM, Asma Tahir <asm...@gm...> wrote:
> Hi Raik,
>
> BINGO! Thank you so much for your full support! It is fully installed.
>
> Just a question, as it is mentioned in the syntax:
>
> search_sequences.py [-q |target.fasta| -o |outFolder| -log |logFile| -db
> |database| -e |e-value-cutoff| -aln |n_alignments| -psi]
>
> about database, how can we direct them to the online database? like
> SwissProt etc or NCBI? or we have to create manually the database?

We have a method in Biskit/Mod/SequenceSearcher that implements remote
blast searches (via BioPython). There are two test cases for this
method in the python module and last time I tested it, it still worked
fine. However, we never included this remote option in the general
modeling work flow. The problem is that we still need the local
database for fetching the actual sequence record. Currently
SequenceSearcher uses the local 'fastacmd' program for that. We never
implemented a remote alternative for this function. It shouldn't be
very difficult though.

The important code to look at is def fastaRecordFromId( self, db, id )
within SequenceSearcher.py. So you would basically need to write an
alternative method that takes the same input but uses the online
databases. I guess BioPython meanwhile should have some methods in
that direction.

If you manage, please tell me and we can quickly work this function
back into the pipeline. I am not sure when I will fnd the time to do
it myself...

Thanks and Good Luck (and Happy New Year!),
Raik

>
> Please let me know also about any online forum or blog related to Biskit
> release and Q/A.
>
> Thanks once again!
>
> Best Regards,
>
> Asma Ishaq Tahir
> Research Technical Assistant
>
> On Wed, Jan 4, 2012 at 5:12 PM, Raik Gruenberg <rai...@cr...>
> wrote:
>>
>> Hi Amir,
>>
>> that looks good then! Don't worry too much about the PVM error
>> message. It will be rather difficult to get PVM installed on a windows
>> system anyway. It can already be quite painful even on Linux. If you
>> are annoyed by it, simply edit Biskit/PVM/__init__.py and switch off
>> the message by commenting out:
>>
>> if not pvm_installed:
>>    EHandler.warning('Could not import PVM (Parallel Virtual Machine)
>> modules.'+
>>        ' Please check that PVM and pypvm are installed!\n'+
>>        '\tParallelisation is not available.')
>>
>> Biskit also works very well without Biggles but several modules use
>> Biggles for making nice plots so it would be nice to get it running.
>> The basic idea is to install the plotutils library and then you need
>> to compile the biggles library against that. This compilation is
>> automatted in the typical
>> python setup.py build
>> step but it requires compilation tools, like a C-compiler.
>>
>> I have honestly no idea how that works on Windows... If you don't
>> manage to get Biggles running, there is also good plotting methods
>> included in the SciPy package. SciPy surely comes with ready-made
>> windows installers. Just that you will then have to create all your
>> plots from scratch and cannot use the ones that are already built-into
>> Biskit.
>>
>> For very quick and dirty plotting, gnuplot is very useful and is used
>> by some Biskit methods too. So if you just install gnuplot (described
>> in the windows install section on biskit.fr) you will already be able
>> to quickly make some simple scatter,  line plots and histograms.
>> That's actually what I am using most of the time.
>>
>> Hope that helps,
>> Raik
>>
>> On Wed, Jan 4, 2012 at 1:09 AM, Asma Tahir <asm...@gm...> wrote:
>> > Hi Raik,
>> >
>> > Thank you so much for your reply!
>> >
>> > Yup, I am using Windows. Your recommendations helped me a lot but now I
>> > got
>> > stuck at the end.... (I have added the trunk folder in
>> > C:\Python27\lib\site-packages\Biskit)
>> >
>> > When I type import Biskit in python, it will give me following error
>> > message:
>> >
>> > Warning: Could not import PVM (Parallel Virtual Machine) modules. Please
>> > check that pvm and pypvm are installed.
>> > Warning: Could not import biggles module. Plotting is not available.
>> >
>> > Biggles and PVM is already in the Trunk folder (The one I put in Biskit
>> > folder).
>> >
>> > For the other two commands (for numpy and Scientific), no error message
>> > at
>> > all.
>> >
>> > Please advice.
>> >
>> > Thank You and Best Regards,
>> >
>> > Asma Ishaq Tahir
>> > Research Technical Assistant
>> >
>> > On Wed, Jan 4, 2012 at 5:44 AM, Raik Gruenberg <rai...@cr...>
>> > wrote:
>> >>
>> >> Hi Asma,
>> >>
>> >> you are trying a Windows installation, right? I haven't tested that in
>> >> a very long time. In any case, the current installation packages on
>> >> sourceforge are rather out of date. I have started working on a new
>> >> release but hadn't the time yet to finish it.
>> >>
>> >> On Windows, your best bet for the moment is to install things manually:
>> >> 1) python
>> >> 2) numpy
>> >> 3) scientific python
>> >> As briefly described on
>> >> http://biskit.pasteur.fr/install/windows_install/ but you should of
>> >> course use more recent versions of everything.
>> >>
>> >> Make sure that numpy and Scientific Python can be used from the python
>> >> you installed. E.g. open an a python interpreter and enter:
>> >>
>> >> import numpy
>> >> import Scientific
>> >>
>> >> Both should run through without error messages.
>> >>
>> >> Then use SVN to retrieve the current development snapshot of biskit.
>> >> There are also some graphical tools. Or you download and unpack the
>> >> daily source tarball from Sourceforge:
>> >> http://biskit.svn.sourceforge.net/viewvc/biskit/trunk/?view=tar
>> >>
>> >> Unpack the content of this archive file into a folder named
>> >> 'biskitproject' or similar. And then add the folder
>> >> C:\....biskitproject/Biskit to your PYTHONPATH.
>> >>
>> >> python
>> >> import Biskit
>> >>
>> >> should then work (the first time, you will receive messages about
>> >> config files that are being created).
>> >>
>> >>
>> >> One note of caution -- Biskit on Windows is rather untested territory.
>> >> I suspect that many of the third-party software wrappers will probably
>> >> not work.
>> >>
>> >> I hope this is helping somewhat. Please tell me if you get it running.
>> >> Perhaps you could then help to update the installation section on the
>> >> web site.
>> >>
>> >> Greetings,
>> >> Raik
>> >>
>> >>
>> >> On Tue, Jan 3, 2012 at 2:26 AM, Asma Tahir <asm...@gm...>
>> >> wrote:
>> >> > Greetings!
>> >> >
>> >> > I encountered problem in installing biskit. I have already installed
>> >> > python
>> >> > 2.5 but numpy is unable to found the python 2.5 in registry. I also
>> >> > have
>> >> > python 2.7. Biskit.exe can recognize only python 2.7 but not python
>> >> > 2.5.
>> >> >
>> >> > Kindly advice.
>> >> >
>> >> > Thank you and Best Regards,
>> >> >
>> >> >
>> >> > *Asma Ishaq Tahir*
>> >> > *Research Technical Assistant*
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a
>> >> > complex
>> >> > infrastructure or vast IT resources to deliver seamless, secure
>> >> > access
>> >> > to
>> >> > virtual desktops. With this all-in-one solution, easily deploy
>> >> > virtual
>> >> > desktops for less than the cost of PCs and save 60% on VDI
>> >> > infrastructure
>> >> > costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>> >> > _______________________________________________
>> >> > 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
>> ___________________________________
>
>



-- 
--
___________________________________
Raik Grünberg
http://www.raiks.de/contact.html
___________________________________

Re: [Biskit-general] Problem in Installing Biskit

[Raik G. <rai...@cr...>]

Hi Amir,

that looks good then! Don't worry too much about the PVM error
message. It will be rather difficult to get PVM installed on a windows
system anyway. It can already be quite painful even on Linux. If you
are annoyed by it, simply edit Biskit/PVM/__init__.py and switch off
the message by commenting out:

if not pvm_installed:
    EHandler.warning('Could not import PVM (Parallel Virtual Machine) modules.'+
        ' Please check that PVM and pypvm are installed!\n'+
        '\tParallelisation is not available.')

Biskit also works very well without Biggles but several modules use
Biggles for making nice plots so it would be nice to get it running.
The basic idea is to install the plotutils library and then you need
to compile the biggles library against that. This compilation is
automatted in the typical
python setup.py build
step but it requires compilation tools, like a C-compiler.

I have honestly no idea how that works on Windows... If you don't
manage to get Biggles running, there is also good plotting methods
included in the SciPy package. SciPy surely comes with ready-made
windows installers. Just that you will then have to create all your
plots from scratch and cannot use the ones that are already built-into
Biskit.

For very quick and dirty plotting, gnuplot is very useful and is used
by some Biskit methods too. So if you just install gnuplot (described
in the windows install section on biskit.fr) you will already be able
to quickly make some simple scatter,  line plots and histograms.
That's actually what I am using most of the time.

Hope that helps,
Raik

On Wed, Jan 4, 2012 at 1:09 AM, Asma Tahir <asm...@gm...> wrote:
> Hi Raik,
>
> Thank you so much for your reply!
>
> Yup, I am using Windows. Your recommendations helped me a lot but now I got
> stuck at the end.... (I have added the trunk folder in
> C:\Python27\lib\site-packages\Biskit)
>
> When I type import Biskit in python, it will give me following error
> message:
>
> Warning: Could not import PVM (Parallel Virtual Machine) modules. Please
> check that pvm and pypvm are installed.
> Warning: Could not import biggles module. Plotting is not available.
>
> Biggles and PVM is already in the Trunk folder (The one I put in Biskit
> folder).
>
> For the other two commands (for numpy and Scientific), no error message at
> all.
>
> Please advice.
>
> Thank You and Best Regards,
>
> Asma Ishaq Tahir
> Research Technical Assistant
>
> On Wed, Jan 4, 2012 at 5:44 AM, Raik Gruenberg <rai...@cr...>
> wrote:
>>
>> Hi Asma,
>>
>> you are trying a Windows installation, right? I haven't tested that in
>> a very long time. In any case, the current installation packages on
>> sourceforge are rather out of date. I have started working on a new
>> release but hadn't the time yet to finish it.
>>
>> On Windows, your best bet for the moment is to install things manually:
>> 1) python
>> 2) numpy
>> 3) scientific python
>> As briefly described on
>> http://biskit.pasteur.fr/install/windows_install/ but you should of
>> course use more recent versions of everything.
>>
>> Make sure that numpy and Scientific Python can be used from the python
>> you installed. E.g. open an a python interpreter and enter:
>>
>> import numpy
>> import Scientific
>>
>> Both should run through without error messages.
>>
>> Then use SVN to retrieve the current development snapshot of biskit.
>> There are also some graphical tools. Or you download and unpack the
>> daily source tarball from Sourceforge:
>> http://biskit.svn.sourceforge.net/viewvc/biskit/trunk/?view=tar
>>
>> Unpack the content of this archive file into a folder named
>> 'biskitproject' or similar. And then add the folder
>> C:\....biskitproject/Biskit to your PYTHONPATH.
>>
>> python
>> import Biskit
>>
>> should then work (the first time, you will receive messages about
>> config files that are being created).
>>
>>
>> One note of caution -- Biskit on Windows is rather untested territory.
>> I suspect that many of the third-party software wrappers will probably
>> not work.
>>
>> I hope this is helping somewhat. Please tell me if you get it running.
>> Perhaps you could then help to update the installation section on the
>> web site.
>>
>> Greetings,
>> Raik
>>
>>
>> On Tue, Jan 3, 2012 at 2:26 AM, Asma Tahir <asm...@gm...> wrote:
>> > Greetings!
>> >
>> > I encountered problem in installing biskit. I have already installed
>> > python
>> > 2.5 but numpy is unable to found the python 2.5 in registry. I also have
>> > python 2.7. Biskit.exe can recognize only python 2.7 but not python 2.5.
>> >
>> > Kindly advice.
>> >
>> > Thank you and Best Regards,
>> >
>> >
>> > *Asma Ishaq Tahir*
>> > *Research Technical Assistant*
>> >
>> > ------------------------------------------------------------------------------
>> > Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a
>> > complex
>> > infrastructure or vast IT resources to deliver seamless, secure access
>> > to
>> > virtual desktops. With this all-in-one solution, easily deploy virtual
>> > desktops for less than the cost of PCs and save 60% on VDI
>> > infrastructure
>> > costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>> > _______________________________________________
>> > 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
___________________________________

Re: [Biskit-general] Problem in Installing Biskit

[Raik G. <rai...@cr...>]

Hi Asma,

you are trying a Windows installation, right? I haven't tested that in
a very long time. In any case, the current installation packages on
sourceforge are rather out of date. I have started working on a new
release but hadn't the time yet to finish it.

On Windows, your best bet for the moment is to install things manually:
1) python
2) numpy
3) scientific python
As briefly described on
http://biskit.pasteur.fr/install/windows_install/ but you should of
course use more recent versions of everything.

Make sure that numpy and Scientific Python can be used from the python
you installed. E.g. open an a python interpreter and enter:

import numpy
import Scientific

Both should run through without error messages.

Then use SVN to retrieve the current development snapshot of biskit.
There are also some graphical tools. Or you download and unpack the
daily source tarball from Sourceforge:
http://biskit.svn.sourceforge.net/viewvc/biskit/trunk/?view=tar

Unpack the content of this archive file into a folder named
'biskitproject' or similar. And then add the folder
C:\....biskitproject/Biskit to your PYTHONPATH.

python
import Biskit

should then work (the first time, you will receive messages about
config files that are being created).


One note of caution -- Biskit on Windows is rather untested territory.
I suspect that many of the third-party software wrappers will probably
not work.

I hope this is helping somewhat. Please tell me if you get it running.
Perhaps you could then help to update the installation section on the
web site.

Greetings,
Raik


On Tue, Jan 3, 2012 at 2:26 AM, Asma Tahir <asm...@gm...> wrote:
> Greetings!
>
> I encountered problem in installing biskit. I have already installed python
> 2.5 but numpy is unable to found the python 2.5 in registry. I also have
> python 2.7. Biskit.exe can recognize only python 2.7 but not python 2.5.
>
> Kindly advice.
>
> Thank you and Best Regards,
>
>
> *Asma Ishaq Tahir*
> *Research Technical Assistant*
> ------------------------------------------------------------------------------
> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> infrastructure or vast IT resources to deliver seamless, secure access to
> virtual desktops. With this all-in-one solution, easily deploy virtual
> desktops for less than the cost of PCs and save 60% on VDI infrastructure
> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
> _______________________________________________
> Biskit-general mailing list
> Bis...@li...
> https://lists.sourceforge.net/lists/listinfo/biskit-general



-- 
--
___________________________________
Raik Grünberg
http://www.raiks.de/contact.html
___________________________________

[Biskit-general] Problem in Installing Biskit

[Asma T. <asm...@gm...>]

Greetings!

I encountered problem in installing biskit. I have already installed python
2.5 but numpy is unable to found the python 2.5 in registry. I also have
python 2.7. Biskit.exe can recognize only python 2.7 but not python 2.5.

Kindly advice.

Thank you and Best Regards,


*Asma Ishaq Tahir*
*Research Technical Assistant*

Re: [Biskit-general] entropy

[Carra, C. (JSC-SK)[Affiliate] <cla...@na...>]

Hi Raik, 
I've tried everything but nothing seems to work.
I keep getting the same error. 

I'm not sure what should i change on 
AmberCrdEntropist.py
the variables look ok to me. 

the amber version I use is amber 9 and 10 and 11. 
it fails in all of them. 
the ptraj output for amber9 and amber10 I guess is the same of amber 8. 
still pretty old, I've attached it in my previous email. 

do you have a ptraj output from amber7? I can check the difference. 
we keep the updated version because amber is so cheap, and the gpu
version is amazingly fast. Anyway, if the nice landscapes from Patagonia
give you some insiration on this issue, please let me know.
take care
claudio

------------------------------------------- 

-----Original Message-----
From: rai...@gm... [mailto:rai...@gm...] On Behalf Of Raik Gruenberg
Sent: Saturday, March 05, 2011 1:24 PM
To: Carra, Claudio (JSC-SK)[Affiliate]
Cc: bis...@li...
Subject: Re: [Biskit-general] entropy

Hi once more,

for the possible parsing problem, I am afraid you will have to play
around yourself a little more. The parsing is done in the low-level
ptraj wrapper AmberCrdEntropist.py:

http://biskit.svn.sourceforge.net/viewvc/biskit/trunk/Biskit/AmberCrdEntropist.py?revision=742&view=markup

The actual parsing starts in line 144

Please check whether the actual ptraj output still matches the
patterns defined there. The error you are reporting indicates that at
least one of the lines has changed.

There is a little test code fragment in the main body of the module
but its not a proper test case and you will have to supply your own
crd and ptraj output to it. But it´s probably a good starting point to
first establish your own test case for this module.

Good luck and tell me how it goes. Please post successful
modifications to a bug report as before. Don´t hesitate to report
failures either.
Greetings from Patagonia,
Raik

[...]

Re: [Biskit-general] entropy

[Raik G. <rai...@cr...>]

Hi once more,

for the possible parsing problem, I am afraid you will have to play
around yourself a little more. The parsing is done in the low-level
ptraj wrapper AmberCrdEntropist.py:

http://biskit.svn.sourceforge.net/viewvc/biskit/trunk/Biskit/AmberCrdEntropist.py?revision=742&view=markup

The actual parsing starts in line 144

Please check whether the actual ptraj output still matches the
patterns defined there. The error you are reporting indicates that at
least one of the lines has changed.

There is a little test code fragment in the main body of the module
but its not a proper test case and you will have to supply your own
crd and ptraj output to it. But it´s probably a good starting point to
first establish your own test case for this module.

Good luck and tell me how it goes. Please post successful
modifications to a bug report as before. Don´t hesitate to report
failures either.
Greetings from Patagonia,
Raik

On Fri, Mar 4, 2011 at 11:10 PM, Raik Gruenberg <rai...@cr...> wrote:
> Hi again Carra,
>
> thanks for the detailed report. I´ll look into it in more detail. Some
> first impression:
>
> On Fri, Mar 4, 2011 at 5:23 PM, Carra, Claudio (JSC-SK)[Affiliate]
> <cla...@na...> wrote:
>> Dear All,
>> I'm trying to calculate the entropy of a flexible complex by using the quasi-harmonic approximation.
>> After the BisKit installation, I run the test and it looked pretty good.
>>
>> ----------
>> SUMMARY:
>> =======
>>
>> A total of 92 tests from 106 modules were run.
>>   - 90 passed
>>   - 2 failed
>>      - error : Biskit.PDBParseNCBI.Test.test_PDBParseModel
>>      - error : Biskit.Dock.Intervor.TestDry.test_IntervorDry
>> DONE
>
> That´s perfect. The intervor test case has to fail. That´s a known
> bug. I don´t know what´s going wrong with the NCBI parser but neither
> of those errors affect the entropy code.
>
>>
>> -----------
>> Before using a_comEntropy.py, I tried to calculate the entropy with the following command
>>
>> a_trajEntropy.py -i dC_1ns_no-Na_ens.dat -o res.dat -ref dC_no-Na.PDBModel  \
>>                 -parm dC_no-Na.top -crd dC_1ns_no-Na.mdcrd -log log -f_out ptraj.out \
>>                 -atoms CA -f_template ptraj.inp -debug -verbose
>>
>> I got the following error:
>>
>> ----------
>> rmsd fitting...#done
>> rmsd fitting...#done
>> rmsd fitting...#done
>> Traceback (most recent call last):
>>  File "/usr/lib/python2.4/site-packages/Biskit/scripts/analysis/a_trajEntropy.py", line 144, in ?
>>    a.run()
>>  File "/usr/lib/python2.4/site-packages/Biskit/Executor.py", line 524, in run
>>    self.finish()
>>  File "/usr/lib/python2.4/site-packages/Biskit/AmberEntropist.py", line 761, in finish
>>    AmberCrdEntropist.finish( self )
>>  File "/usr/lib/python2.4/site-packages/Biskit/AmberCrdEntropist.py", line 131, in finish
>>    self.result = self.parsePtrajResult( self.f_out )
>>  File "/usr/lib/python2.4/site-packages/Biskit/AmberCrdEntropist.py", line 195, in parsePtrajResult
>>    raise EntropistError, 'unexpected end of ptraj output file.'
>> Biskit.AmberCrdEntropist.EntropistError: unexpected end of ptraj output file.
>>
>> ---------
>>
>> however, in ptraj.out I get
>>
>> ---------
>>           freq.         E                  Cv                 S
>>          cm**-1      kcal/mol        cal/mol-kelvin    cal/mol-kelvin
>> --------------------------------------------------------------------------------
>>  Total              7957550.797                nan            196.551
>>  translational             .888              2.979             45.315
>>  rotational                .888              2.979             44.438
>>  vibrational        7957549.021                nan            106.798
>>     1     6.852           .592              1.986              8.755
>>
>> ---------
>
> OK, then it looks as if the output of ptraj has changed between
> versions and the script doesn´t recognice the successful result any
> longer. Should be not too difficult to fix. Could you please file a
> bug at the sourceforge project site? (there is a link on
> biskit.sf.net) Please attach the full ptraj output file.
>
>>
>>
>> So I'm not sure what's wrong.
>> All this if i use a small protein as a sample molecule.
>> If I use a fragment of dna, let's say dC8, things get much worse.
>> I've this error:
>>
>> -------------
>>
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> done
>> Traceback (most recent call last):
>>  File "/usr/lib/python2.4/site-packages/Biskit/scripts/analysis/a_trajEntropy.py", line 143, in ?
>>    a = AmberEntropist( f_in, **options )
>>  File "/usr/lib/python2.4/site-packages/Biskit/AmberEntropist.py", line 192, in __init__
>>    self.traj = self.prepareTraj( traj, self.ref, cast=self.cast )
>>  File "/usr/lib/python2.4/site-packages/Biskit/AmberEntropist.py", line 572, in prepareTraj
>>    self.fit( t, ref )
>>  File "/usr/lib/python2.4/site-packages/Biskit/AmberEntropist.py", line 253, in fit
>>    m_avg = traj[self.fit_s : self.fit_e ].avgModel()
>>  File "/usr/lib/python2.4/site-packages/Biskit/Trajectory.py", line 248, in avgModel
>>    result.setXyz( N.average( self.frames ) )
>>  File "/usr/lib64/python2.4/site-packages/numpy/oldnumeric/functions.py", line 124, in average
>>    return np.average(a, axis, weights, returned)
>>  File "/usr/lib64/python2.4/site-packages/numpy/lib/function_base.py", line 447, in average
>>    scl = avg.dtype.type(a.size/avg.size)
>> ZeroDivisionError: integer division or modulo by zero
>>
>
> Right, I only had proteins in mind when writing the code. Most likely
> I am filtering for protein-only atoms before doing the fit. And then
> there is nothing to fit left for the DNA structure, which then leads
> to the zero-division. This should actually be even easier to fix than
> the other bug.
>
> Have a nice weekend,
> Raik
>
>> ------------
>>
>> I had no prob to generate the traj2ensemble.py trajectories in both cases, and no
>> errors for the corresponding PDBMoldel structures.
>> I'm kind of lost here.
>> If you guys have any idea, I would really appreciate some help
>> thanks for your time
>> Sincerely,
>> Claudio
>>
>>
>>
>> ------------------------------------------------------------------------------
>> What You Don't Know About Data Connectivity CAN Hurt You
>> This paper provides an overview of data connectivity, details
>> its effect on application quality, and explores various alternative
>> solutions. http://p.sf.net/sfu/progress-d2d
>> _______________________________________________
>> Biskit-general mailing list
>> Bis...@li...
>> https://lists.sourceforge.net/lists/listinfo/biskit-general
>>
>

Re: [Biskit-general] entropy

[Raik G. <rai...@cr...>]

On Fri, Mar 4, 2011 at 11:10 PM, Raik Gruenberg <rai...@cr...> wrote:
> Hi again Carra,
>
> thanks for the detailed report. I´ll look into it in more detail. Some
> first impression:
>
> On Fri, Mar 4, 2011 at 5:23 PM, Carra, Claudio (JSC-SK)[Affiliate]
> <cla...@na...> wrote:
>> Dear All,
>> I'm trying to calculate the entropy of a flexible complex by using the quasi-harmonic approximation.
>> After the BisKit installation, I run the test and it looked pretty good.
>>
>> ----------
>> SUMMARY:
>> =======
>>
>> A total of 92 tests from 106 modules were run.
>>   - 90 passed
>>   - 2 failed
>>      - error : Biskit.PDBParseNCBI.Test.test_PDBParseModel
>>      - error : Biskit.Dock.Intervor.TestDry.test_IntervorDry
>> DONE
>
> That´s perfect. The intervor test case has to fail. That´s a known
> bug. I don´t know what´s going wrong with the NCBI parser but neither
> of those errors affect the entropy code.
>
>>
>> -----------
>> Before using a_comEntropy.py, I tried to calculate the entropy with the following command
>>
>> a_trajEntropy.py -i dC_1ns_no-Na_ens.dat -o res.dat -ref dC_no-Na.PDBModel  \
>>                 -parm dC_no-Na.top -crd dC_1ns_no-Na.mdcrd -log log -f_out ptraj.out \
>>                 -atoms CA -f_template ptraj.inp -debug -verbose
>>
>> I got the following error:
>>
>> ----------
>> rmsd fitting...#done
>> rmsd fitting...#done
>> rmsd fitting...#done
>> Traceback (most recent call last):
>>  File "/usr/lib/python2.4/site-packages/Biskit/scripts/analysis/a_trajEntropy.py", line 144, in ?
>>    a.run()
>>  File "/usr/lib/python2.4/site-packages/Biskit/Executor.py", line 524, in run
>>    self.finish()
>>  File "/usr/lib/python2.4/site-packages/Biskit/AmberEntropist.py", line 761, in finish
>>    AmberCrdEntropist.finish( self )
>>  File "/usr/lib/python2.4/site-packages/Biskit/AmberCrdEntropist.py", line 131, in finish
>>    self.result = self.parsePtrajResult( self.f_out )
>>  File "/usr/lib/python2.4/site-packages/Biskit/AmberCrdEntropist.py", line 195, in parsePtrajResult
>>    raise EntropistError, 'unexpected end of ptraj output file.'
>> Biskit.AmberCrdEntropist.EntropistError: unexpected end of ptraj output file.
>>
>> ---------
>>
>> however, in ptraj.out I get
>>
>> ---------
>>           freq.         E                  Cv                 S
>>          cm**-1      kcal/mol        cal/mol-kelvin    cal/mol-kelvin
>> --------------------------------------------------------------------------------
>>  Total              7957550.797                nan            196.551
>>  translational             .888              2.979             45.315
>>  rotational                .888              2.979             44.438
>>  vibrational        7957549.021                nan            106.798
>>     1     6.852           .592              1.986              8.755
>>
>> ---------
>
> OK, then it looks as if the output of ptraj has changed between
> versions and the script doesn´t recognice the successful result any
> longer. Should be not too difficult to fix. Could you please file a
> bug at the sourceforge project site? (there is a link on
> biskit.sf.net) Please attach the full ptraj output file.
>
>>
>>
>> So I'm not sure what's wrong.
>> All this if i use a small protein as a sample molecule.
>> If I use a fragment of dna, let's say dC8, things get much worse.
>> I've this error:
>>
>> -------------
>>
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> done
>> Traceback (most recent call last):
>>  File "/usr/lib/python2.4/site-packages/Biskit/scripts/analysis/a_trajEntropy.py", line 143, in ?
>>    a = AmberEntropist( f_in, **options )
>>  File "/usr/lib/python2.4/site-packages/Biskit/AmberEntropist.py", line 192, in __init__
>>    self.traj = self.prepareTraj( traj, self.ref, cast=self.cast )
>>  File "/usr/lib/python2.4/site-packages/Biskit/AmberEntropist.py", line 572, in prepareTraj
>>    self.fit( t, ref )
>>  File "/usr/lib/python2.4/site-packages/Biskit/AmberEntropist.py", line 253, in fit
>>    m_avg = traj[self.fit_s : self.fit_e ].avgModel()
>>  File "/usr/lib/python2.4/site-packages/Biskit/Trajectory.py", line 248, in avgModel
>>    result.setXyz( N.average( self.frames ) )
>>  File "/usr/lib64/python2.4/site-packages/numpy/oldnumeric/functions.py", line 124, in average
>>    return np.average(a, axis, weights, returned)
>>  File "/usr/lib64/python2.4/site-packages/numpy/lib/function_base.py", line 447, in average
>>    scl = avg.dtype.type(a.size/avg.size)
>> ZeroDivisionError: integer division or modulo by zero
>>
>
> Right, I only had proteins in mind when writing the code. Most likely
> I am filtering for protein-only atoms before doing the fit. And then
> there is nothing to fit left for the DNA structure, which then leads
> to the zero-division. This should actually be even easier to fix than
> the other bug.

Hi Claudio,

let´s first look at the easy problem:

The culprit for the DNA deletion is in Biskit/AmberEntropist.py.
Please have a look at this module. It encapsulates the entropy
calculation protocols and is well documented. I cannot fix it myself
from the internet cafe PC but can only look at the code:
http://biskit.svn.sourceforge.net/viewvc/biskit/trunk/Biskit/AmberEntropist.py?revision=933&view=markup

Check out line 306
306 	 def __cleanAtoms( self, m ):
307 	"""
308 	Remove non protein atoms and H if needed.
310 	@param m: model to clean
311 	@type m: PDBModel
313 	@return: cleaned model
314 	@rtype: PDBModel
315 	"""
316 	m.keep( N.nonzero( m.maskProtein() ) )
317 	if self.heavy:
318 	m.keep( N.nonzero( m.maskHeavy() ) )
319 	return m

(indentation messed up during the paste).
PDBModel.maskProtein returns a mask (of True or False) marking each
atom in the structure that belongs to a protein. numpy.nonzero
converts this into a list of atom positions and PDBModel.keep only
keeps these positions. Best is if you get some interactive python
prompt and play around with these functions yourself. My
recommendation is to change line 316 into:

m.keep( N.nonzero( m.maskProtein() or m.maskDNA() )

That´s getting a bit obfuscated though and I am not completely sure
whether the or operation works the way I think. Alternative:
mask = N.logical_or( m.maskProtein(), m.maskDNA() )
m.keep( mask )

In theory this should be enough to fix the DNA problem. Please test
and tell me how it works. If successful, it would be cool if you could
attach the corrected py file to the bug report -- it¨s going to be two
months before I am back in front of a real work station, would be a
shame if our changes get lost.

Bug reports can be filed here:
http://sourceforge.net/tracker/?group_id=150896&atid=779191

Good luck!
Raik

>
> Have a nice weekend,
> Raik
>
>> ------------
>>
>> I had no prob to generate the traj2ensemble.py trajectories in both cases, and no
>> errors for the corresponding PDBMoldel structures.
>> I'm kind of lost here.
>> If you guys have any idea, I would really appreciate some help
>> thanks for your time
>> Sincerely,
>> Claudio
>>
>>
>>
>> ------------------------------------------------------------------------------
>> What You Don't Know About Data Connectivity CAN Hurt You
>> This paper provides an overview of data connectivity, details
>> its effect on application quality, and explores various alternative
>> solutions. http://p.sf.net/sfu/progress-d2d
>> _______________________________________________
>> Biskit-general mailing list
>> Bis...@li...
>> https://lists.sourceforge.net/lists/listinfo/biskit-general
>>
>