Re: Using multi-processor for model_free

[Troels Emtekær Linnet]

Hi Sam.

Can you try:
mpirun --version

Thanks

2016-10-01 0:00 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> Here is a list of the packages I got off of the fedora package list
> Openmpi:
> openmpi-1.7.3-1.fc.20(64-bit)
> openmpi-devel-1.7.3-1.fc20(64bit)
> pypar-openmpi-2.1.5_108_3.fc.20(64bit)
> python3-mpi4py-1.3.1-1.fc20(64bit)
>
> Mpi4py
> mpi4py-common-1.3.1-1.fc20
> mpi4py-mpich-1.3.1-1.fc20
> mpi4py-openmpi-1.3.1-1.fc20
> python3-mpi4py-mpich-1.3.1-1.fc20
> python3-mpi4py-openmpi-1.3.1-1.fc20
>
> Note: I now know the mpich is extra and pointless. I only use the openmpi
> when I load my modules. I have not compiled or configured anything with
> these packages. I just installed them directly from the package list. If
> you need any more info on what is installed on these computers let me know!
>
> Sincerely,
> Sam
>
>
> On Fri, Sep 30, 2016 at 2:23 PM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Hi Sam.
>>
>> I am trying to setup myself on Google Cloud Platform.
>>
>> Here I setting up for a Redhat 6 distro, in hope it gets close to Fedora
>> 20.
>>
>> I am currently making a deployment script.
>>
>> The process is written here:
>> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computin
>> g#Install_packages_at_server
>>
>> But that is a little old, since the configurations has changed a little
>> since 2015.
>> And the last deployment script is for Ubuntu.
>>
>> Getting the packages right is a pain ;)
>>
>> Let me return when I know some more.
>>
>>
>>
>> 2016-09-30 23:03 GMT+02:00 Mahdi, Sam :
>>
>>> Hi Troels,
>>>
>>> I attempted the full path
>>> mpirun -np 5 ~/relax-4.0.2/relax --multi="mpi4py" -v
>>> and still got the same result. No output.
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Fri, Sep 30, 2016 at 11:43 AM, Troels Emtekær Linnet <
>>> tlin...@nmr-relax.com> wrote:
>>>
 Hi Sam.

 Hm. Alright.

 But to rule it out in my head, can you try this:

 mpirun -np 5 /home/users/software/relax-4.0.2/relax --multi="mpi4py" -v

 Or similar destination path.
 But please try the full path.

 Best
 Troels

 2016-09-30 19:47 GMT+02:00 Mahdi, Sam :

> I get the same results with the full path mpirun -np 5
> ~/relax-4.0.2/relax --multi="mpi4py" -v
> Still no output.
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 10:39 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Sam.
>>
>> All points to:
>> "./relax"   is NOT calling relax in the current folder.
>>
>> It is because the command "mpirun" is running it.
>>
>> Please provide the FULL path to relax.
>>
>> I think I have written this before. ;)
>>
>> Best
>> Troels
>>
>>
>> 2016-09-30 19:24 GMT+02:00 Mahdi, Sam :
>>
>>> Sorry, you're right, I re-ran the mpirun -np 5 ./relax
>>> --multi="mpi4py" -v
>>> and got no output. So I'm just curious for the other computers I
>>> download
>>> openmpi in, just installing it and compiling it isn't enough? There
>>> are
>>> some configurations you have to make to have it run on relax?
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne <
>>> edw...@nmr-relax.com>
>>> wrote:
>>>
>>> > On 30 September 2016 at 19:12, Mahdi, Sam <
>>> sam.mahdi@my.csun.edu>
>>> > wrote:
>>> > > Hi Edward,
>>> > >
>>> > > So I ran the the mpirun commands you suggested. The echo world
>>> works
>>> > fine. I
>>> > > get the same results you did. For the relax one, this is the
>>> output I
>>> > > recieved
>>> > >  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax
>>> 4.0.2
>>> > > Usage: relax [options] [script_file]
>>> > >
>>> > > RelaxError: incorrect number of arguments
>>> >
>>> > Have a close look at my original text:
>>> >
>>> > [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
>>> > --multi="mpi4py" -v
>>> > relax 4.0.2
>>> > [edward@localhost ~]$
>>> >
>>> > Note how "relax 4.0.2" is on a different line - that is the relax
>>> > output, not the command line input.  Try again without that text.
>>> >
>>> >
>>> > > RelaxError: ambiguous option: --v (--verification-tests,
>>> --version?)
>>> >
>>> > This is because the double-dash to single-dash conversion is only
>>> in
>>> > the HTML version of the relax manual, and not emails.  Run "relax
>>> -h"
>>> > to see a description of this option.
>>> >
>>> >
>>> > > Also, the reason its ./relax is because I have relax 2.2.5
>>> installed,
>>> > and I
>>> > > have that set up as an Alias, so if I just type relax, it'll
>>> open up
>>> > relax
>>> > > 2.2.5. So I went to the actual 

Re: relax-users Digest, Vol 116, Issue 38

[Mahdi, Sam]

Hi Edward,

So when I ran it as read_mol=0, it gave me the same error. But it worked
once I changed it to read_mol=1. I thought mol=0 was for set A and mol=1
was for set B?

Sincerely,
Sam

On Fri, Sep 30, 2016 at 2:00 PM, Mahdi, Sam 
wrote:

> Hi Edward,
>
> The protein itself is a monomer/dimer mix, normally it is a monomer;
> however, the concentrations at which we observe it at (NMR concentrations
> are around 1mM, the protein forms a dimer (primarily). Using titration
> experiments we have found what looks to be an interface (using CSP), and
> have used a docking program to show what the dimer would look like in
> regards to the dimer interface and what is geometrically/energetically
> possible. So we aren't looking for proof of a dimer, but my PI had informed
> me that our S^2 would not be accurate if we used the pdb of the monomer
> (due to slower tumbling effecting our relaxation data, basically having
> data for a dimer, and thus the pdb file must also account for the larger
> size/slower tumbling, basically since the data is for a dimer, the pdb
> file/structure should also be that of a dimer so they correlate). However,
> if the S^2 data doesn't get effected too much whether it is a dimer or
> monomer, then I guess it doesn't matter too much in this case.
>
> Also, could you tell me the exact modification I need to make to my
> script?
> This is what it was before
> structure.read_pdb('cluster1_12.pdb',set_mol_name='hRGS4')
> Is this what I should modify it to?
> structure.read_pdb('cluster1_12.pdb',set_mol_name='hRGS4',read_mol=0)
>
>
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 11:45 AM, Edward d'Auvergne 
> wrote:
>
>> On 30 September 2016 at 19:45, Mahdi, Sam 
>> wrote:
>> > Sorry, I just want to make sure I fully understand this so I can
>> explain it
>> > to my PI:
>>
>> No problems, this is by far the most complicated aspect in the field of
>> NMR ;)
>>
>>
>> > So if there is symmetry, I can upload the same pdb file with the dimer
>> (set
>> > A and B) but tell it to read only one set.
>>
>> Load rather than upload, but yes.
>>
>>
>> > Since S^2 isn't effected too much
>> > versus a dimer versus a monomer, the only thing that is important is the
>> > change in co-ordinates of one set of the dimer (i.e. the differnence in
>> > co-ordinates between set A in a monomer, and set A in a dimer
>> co-ordinates,
>> > or set A in a different version of that dimer's co-ordinates).
>>
>> S2 is not affected by the reference frame.  This only matters for
>> comparing diffusion tensors.  Though you will only ever see one
>> tensor, as that is what is in your NMR sample (if you have a
>> monomer-dimer mix, then you're in trouble and will see a lot of
>> artificial Rex and ns motions).
>>
>>
>> > I say this
>> > because I have already run my protein's data with the pdb structure of
>> the
>> > monomer, and I have 2 different pdb files the docking program gave back
>> for
>> > the dimer (2 different ways the dimer could form from one interface).
>>
>> Well, your analysis will always return the same diffusion tensor.  If
>> you want these diffusion tensors to all be in the same frame, use the
>> relax structure.superimpose user function with the method='fit to
>> first' argument.  Then just pick which will be your reference
>> structure and superimpose.  You can superimpose A and B - separately -
>> onto the monomer frame.
>>
>> Let's pick the monomer as the reference frame.  Then:
>>
>> - If you superimpose "dimer 1, struct A" to the monomer, you
>> should find the same tensor.
>> - If you superimpose "dimer 1, struct B" to the monomer, you
>> should find the same tensor.
>> - If you superimpose "dimer 2, struct A" to the monomer, you
>> should find the same tensor.
>> - If you superimpose "dimer 2, struct B" to the monomer, you
>> should find the same tensor.
>>
>> If the docking program did not optimise the internal monomer
>> structure, you will get identical results.  Otherwise you'll see minor
>> internal motion changes.  If your PI was hoping that you would be able
>> to tell him that you have a monomer or one of the 2 dimers in your NMR
>> tube, well then you will need to start to read many, many papers on
>> diffusion tensor prediction.  But know that all prediction methods
>> underestimate the diffusion tensor (e.g. David Case is working on this
>> exact problem for MD simulations).  In this case, relaxation data is
>> not the best NMR method for this.  It would be better to use RDCs from
>> a purely steric alignment and to compare that to what PALES prediction
>> comes up with (though that itself is still a very rough and imperfect
>> method).
>>
>> Regards,
>>
>> Edward
>>
>
>
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Re: Using multi-processor for model_free

[Troels Emtekær Linnet]

Hi Sam.

I am trying to setup myself on Google Cloud Platform.

Here I setting up for a Redhat 6 distro, in hope it gets close to Fedora 20.

I am currently making a deployment script.

The process is written here:
http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computing#Install_packages_at_server

But that is a little old, since the configurations has changed a little
since 2015.
And the last deployment script is for Ubuntu.

Getting the packages right is a pain ;)

Let me return when I know some more.



2016-09-30 23:03 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> I attempted the full path
> mpirun -np 5 ~/relax-4.0.2/relax --multi="mpi4py" -v
> and still got the same result. No output.
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 11:43 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Hi Sam.
>>
>> Hm. Alright.
>>
>> But to rule it out in my head, can you try this:
>>
>> mpirun -np 5 /home/users/software/relax-4.0.2/relax --multi="mpi4py" -v
>>
>> Or similar destination path.
>> But please try the full path.
>>
>> Best
>> Troels
>>
>> 2016-09-30 19:47 GMT+02:00 Mahdi, Sam :
>>
>>> I get the same results with the full path mpirun -np 5
>>> ~/relax-4.0.2/relax --multi="mpi4py" -v
>>> Still no output.
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Fri, Sep 30, 2016 at 10:39 AM, Troels Emtekær Linnet <
>>> tlin...@nmr-relax.com> wrote:
>>>
 Sam.

 All points to:
 "./relax"   is NOT calling relax in the current folder.

 It is because the command "mpirun" is running it.

 Please provide the FULL path to relax.

 I think I have written this before. ;)

 Best
 Troels


 2016-09-30 19:24 GMT+02:00 Mahdi, Sam :

> Sorry, you're right, I re-ran the mpirun -np 5 ./relax
> --multi="mpi4py" -v
> and got no output. So I'm just curious for the other computers I
> download
> openmpi in, just installing it and compiling it isn't enough? There are
> some configurations you have to make to have it run on relax?
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne <
> edw...@nmr-relax.com>
> wrote:
>
> > On 30 September 2016 at 19:12, Mahdi, Sam  >
> > wrote:
> > > Hi Edward,
> > >
> > > So I ran the the mpirun commands you suggested. The echo world
> works
> > fine. I
> > > get the same results you did. For the relax one, this is the
> output I
> > > recieved
> > >  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax
> 4.0.2
> > > Usage: relax [options] [script_file]
> > >
> > > RelaxError: incorrect number of arguments
> >
> > Have a close look at my original text:
> >
> > [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
> > --multi="mpi4py" -v
> > relax 4.0.2
> > [edward@localhost ~]$
> >
> > Note how "relax 4.0.2" is on a different line - that is the relax
> > output, not the command line input.  Try again without that text.
> >
> >
> > > RelaxError: ambiguous option: --v (--verification-tests,
> --version?)
> >
> > This is because the double-dash to single-dash conversion is only in
> > the HTML version of the relax manual, and not emails.  Run "relax -h"
> > to see a description of this option.
> >
> >
> > > Also, the reason its ./relax is because I have relax 2.2.5
> installed,
> > and I
> > > have that set up as an Alias, so if I just type relax, it'll open
> up
> > relax
> > > 2.2.5. So I went to the actual relax-4.0.2. directory instead of
> > indicating
> > > its path and just typed ./relax. (By I, I mean the administrator
> of this
> > > computer, I do not have root access to this computer).
> >
> > You should set your alias to the relax-4.0.2 version instead.  The
> > 2.2.5 version is very, very old, and many bugs have been fixed since
> > then.
> >
> > Regards,
> >
> > Edward
> >
> ___
> relax (http://www.nmr-relax.com)
>
> This is the relax-users mailing list
> relax-users@gna.org
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
> https://mail.gna.org/listinfo/relax-users
>


>>>
>>
>
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Re: Using multi-processor for model_free

[Mahdi, Sam]

Hi Troels,

I attempted the full path
mpirun -np 5 ~/relax-4.0.2/relax --multi="mpi4py" -v
and still got the same result. No output.

Sincerely,
Sam

On Fri, Sep 30, 2016 at 11:43 AM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> Hm. Alright.
>
> But to rule it out in my head, can you try this:
>
> mpirun -np 5 /home/users/software/relax-4.0.2/relax --multi="mpi4py" -v
>
> Or similar destination path.
> But please try the full path.
>
> Best
> Troels
>
> 2016-09-30 19:47 GMT+02:00 Mahdi, Sam :
>
>> I get the same results with the full path mpirun -np 5
>> ~/relax-4.0.2/relax --multi="mpi4py" -v
>> Still no output.
>>
>> Sincerely,
>> Sam
>>
>> On Fri, Sep 30, 2016 at 10:39 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Sam.
>>>
>>> All points to:
>>> "./relax"   is NOT calling relax in the current folder.
>>>
>>> It is because the command "mpirun" is running it.
>>>
>>> Please provide the FULL path to relax.
>>>
>>> I think I have written this before. ;)
>>>
>>> Best
>>> Troels
>>>
>>>
>>> 2016-09-30 19:24 GMT+02:00 Mahdi, Sam :
>>>
 Sorry, you're right, I re-ran the mpirun -np 5 ./relax --multi="mpi4py"
 -v
 and got no output. So I'm just curious for the other computers I
 download
 openmpi in, just installing it and compiling it isn't enough? There are
 some configurations you have to make to have it run on relax?

 Sincerely,
 Sam

 On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne <
 edw...@nmr-relax.com>
 wrote:

 > On 30 September 2016 at 19:12, Mahdi, Sam 
 > wrote:
 > > Hi Edward,
 > >
 > > So I ran the the mpirun commands you suggested. The echo world works
 > fine. I
 > > get the same results you did. For the relax one, this is the output
 I
 > > recieved
 > >  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax
 4.0.2
 > > Usage: relax [options] [script_file]
 > >
 > > RelaxError: incorrect number of arguments
 >
 > Have a close look at my original text:
 >
 > [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
 > --multi="mpi4py" -v
 > relax 4.0.2
 > [edward@localhost ~]$
 >
 > Note how "relax 4.0.2" is on a different line - that is the relax
 > output, not the command line input.  Try again without that text.
 >
 >
 > > RelaxError: ambiguous option: --v (--verification-tests, --version?)
 >
 > This is because the double-dash to single-dash conversion is only in
 > the HTML version of the relax manual, and not emails.  Run "relax -h"
 > to see a description of this option.
 >
 >
 > > Also, the reason its ./relax is because I have relax 2.2.5
 installed,
 > and I
 > > have that set up as an Alias, so if I just type relax, it'll open up
 > relax
 > > 2.2.5. So I went to the actual relax-4.0.2. directory instead of
 > indicating
 > > its path and just typed ./relax. (By I, I mean the administrator of
 this
 > > computer, I do not have root access to this computer).
 >
 > You should set your alias to the relax-4.0.2 version instead.  The
 > 2.2.5 version is very, very old, and many bugs have been fixed since
 > then.
 >
 > Regards,
 >
 > Edward
 >
 ___
 relax (http://www.nmr-relax.com)

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 relax-users@gna.org

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 reminder, or change your subscription options,
 visit the list information page at
 https://mail.gna.org/listinfo/relax-users

>>>
>>>
>>
>
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Re: relax-users Digest, Vol 116, Issue 38

[Mahdi, Sam]

Hi Edward,

The protein itself is a monomer/dimer mix, normally it is a monomer;
however, the concentrations at which we observe it at (NMR concentrations
are around 1mM, the protein forms a dimer (primarily). Using titration
experiments we have found what looks to be an interface (using CSP), and
have used a docking program to show what the dimer would look like in
regards to the dimer interface and what is geometrically/energetically
possible. So we aren't looking for proof of a dimer, but my PI had informed
me that our S^2 would not be accurate if we used the pdb of the monomer
(due to slower tumbling effecting our relaxation data, basically having
data for a dimer, and thus the pdb file must also account for the larger
size/slower tumbling, basically since the data is for a dimer, the pdb
file/structure should also be that of a dimer so they correlate). However,
if the S^2 data doesn't get effected too much whether it is a dimer or
monomer, then I guess it doesn't matter too much in this case.

Also, could you tell me the exact modification I need to make to my script?
This is what it was before
structure.read_pdb('cluster1_12.pdb',set_mol_name='hRGS4')
Is this what I should modify it to?
structure.read_pdb('cluster1_12.pdb',set_mol_name='hRGS4',read_mol=0)



Sincerely,
Sam

On Fri, Sep 30, 2016 at 11:45 AM, Edward d'Auvergne 
wrote:

> On 30 September 2016 at 19:45, Mahdi, Sam 
> wrote:
> > Sorry, I just want to make sure I fully understand this so I can explain
> it
> > to my PI:
>
> No problems, this is by far the most complicated aspect in the field of
> NMR ;)
>
>
> > So if there is symmetry, I can upload the same pdb file with the dimer
> (set
> > A and B) but tell it to read only one set.
>
> Load rather than upload, but yes.
>
>
> > Since S^2 isn't effected too much
> > versus a dimer versus a monomer, the only thing that is important is the
> > change in co-ordinates of one set of the dimer (i.e. the differnence in
> > co-ordinates between set A in a monomer, and set A in a dimer
> co-ordinates,
> > or set A in a different version of that dimer's co-ordinates).
>
> S2 is not affected by the reference frame.  This only matters for
> comparing diffusion tensors.  Though you will only ever see one
> tensor, as that is what is in your NMR sample (if you have a
> monomer-dimer mix, then you're in trouble and will see a lot of
> artificial Rex and ns motions).
>
>
> > I say this
> > because I have already run my protein's data with the pdb structure of
> the
> > monomer, and I have 2 different pdb files the docking program gave back
> for
> > the dimer (2 different ways the dimer could form from one interface).
>
> Well, your analysis will always return the same diffusion tensor.  If
> you want these diffusion tensors to all be in the same frame, use the
> relax structure.superimpose user function with the method='fit to
> first' argument.  Then just pick which will be your reference
> structure and superimpose.  You can superimpose A and B - separately -
> onto the monomer frame.
>
> Let's pick the monomer as the reference frame.  Then:
>
> - If you superimpose "dimer 1, struct A" to the monomer, you
> should find the same tensor.
> - If you superimpose "dimer 1, struct B" to the monomer, you
> should find the same tensor.
> - If you superimpose "dimer 2, struct A" to the monomer, you
> should find the same tensor.
> - If you superimpose "dimer 2, struct B" to the monomer, you
> should find the same tensor.
>
> If the docking program did not optimise the internal monomer
> structure, you will get identical results.  Otherwise you'll see minor
> internal motion changes.  If your PI was hoping that you would be able
> to tell him that you have a monomer or one of the 2 dimers in your NMR
> tube, well then you will need to start to read many, many papers on
> diffusion tensor prediction.  But know that all prediction methods
> underestimate the diffusion tensor (e.g. David Case is working on this
> exact problem for MD simulations).  In this case, relaxation data is
> not the best NMR method for this.  It would be better to use RDCs from
> a purely steric alignment and to compare that to what PALES prediction
> comes up with (though that itself is still a very rough and imperfect
> method).
>
> Regards,
>
> Edward
>
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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 30 September 2016 at 19:45, Mahdi, Sam  wrote:
> Sorry, I just want to make sure I fully understand this so I can explain it
> to my PI:

No problems, this is by far the most complicated aspect in the field of NMR ;)


> So if there is symmetry, I can upload the same pdb file with the dimer (set
> A and B) but tell it to read only one set.

Load rather than upload, but yes.


> Since S^2 isn't effected too much
> versus a dimer versus a monomer, the only thing that is important is the
> change in co-ordinates of one set of the dimer (i.e. the differnence in
> co-ordinates between set A in a monomer, and set A in a dimer co-ordinates,
> or set A in a different version of that dimer's co-ordinates).

S2 is not affected by the reference frame.  This only matters for
comparing diffusion tensors.  Though you will only ever see one
tensor, as that is what is in your NMR sample (if you have a
monomer-dimer mix, then you're in trouble and will see a lot of
artificial Rex and ns motions).


> I say this
> because I have already run my protein's data with the pdb structure of the
> monomer, and I have 2 different pdb files the docking program gave back for
> the dimer (2 different ways the dimer could form from one interface).

Well, your analysis will always return the same diffusion tensor.  If
you want these diffusion tensors to all be in the same frame, use the
relax structure.superimpose user function with the method='fit to
first' argument.  Then just pick which will be your reference
structure and superimpose.  You can superimpose A and B - separately -
onto the monomer frame.

Let's pick the monomer as the reference frame.  Then:

- If you superimpose "dimer 1, struct A" to the monomer, you
should find the same tensor.
- If you superimpose "dimer 1, struct B" to the monomer, you
should find the same tensor.
- If you superimpose "dimer 2, struct A" to the monomer, you
should find the same tensor.
- If you superimpose "dimer 2, struct B" to the monomer, you
should find the same tensor.

If the docking program did not optimise the internal monomer
structure, you will get identical results.  Otherwise you'll see minor
internal motion changes.  If your PI was hoping that you would be able
to tell him that you have a monomer or one of the 2 dimers in your NMR
tube, well then you will need to start to read many, many papers on
diffusion tensor prediction.  But know that all prediction methods
underestimate the diffusion tensor (e.g. David Case is working on this
exact problem for MD simulations).  In this case, relaxation data is
not the best NMR method for this.  It would be better to use RDCs from
a purely steric alignment and to compare that to what PALES prediction
comes up with (though that itself is still a very rough and imperfect
method).

Regards,

Edward

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Re: Using multi-processor for model_free

[Troels Emtekær Linnet]

Hi Sam.

Hm. Alright.

But to rule it out in my head, can you try this:

mpirun -np 5 /home/users/software/relax-4.0.2/relax --multi="mpi4py" -v

Or similar destination path.
But please try the full path.

Best
Troels

2016-09-30 19:47 GMT+02:00 Mahdi, Sam :

> I get the same results with the full path mpirun -np 5 ~/relax-4.0.2/relax
> --multi="mpi4py" -v
> Still no output.
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 10:39 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Sam.
>>
>> All points to:
>> "./relax"   is NOT calling relax in the current folder.
>>
>> It is because the command "mpirun" is running it.
>>
>> Please provide the FULL path to relax.
>>
>> I think I have written this before. ;)
>>
>> Best
>> Troels
>>
>>
>> 2016-09-30 19:24 GMT+02:00 Mahdi, Sam :
>>
>>> Sorry, you're right, I re-ran the mpirun -np 5 ./relax --multi="mpi4py"
>>> -v
>>> and got no output. So I'm just curious for the other computers I download
>>> openmpi in, just installing it and compiling it isn't enough? There are
>>> some configurations you have to make to have it run on relax?
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne <
>>> edw...@nmr-relax.com>
>>> wrote:
>>>
>>> > On 30 September 2016 at 19:12, Mahdi, Sam 
>>> > wrote:
>>> > > Hi Edward,
>>> > >
>>> > > So I ran the the mpirun commands you suggested. The echo world works
>>> > fine. I
>>> > > get the same results you did. For the relax one, this is the output I
>>> > > recieved
>>> > >  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax
>>> 4.0.2
>>> > > Usage: relax [options] [script_file]
>>> > >
>>> > > RelaxError: incorrect number of arguments
>>> >
>>> > Have a close look at my original text:
>>> >
>>> > [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
>>> > --multi="mpi4py" -v
>>> > relax 4.0.2
>>> > [edward@localhost ~]$
>>> >
>>> > Note how "relax 4.0.2" is on a different line - that is the relax
>>> > output, not the command line input.  Try again without that text.
>>> >
>>> >
>>> > > RelaxError: ambiguous option: --v (--verification-tests, --version?)
>>> >
>>> > This is because the double-dash to single-dash conversion is only in
>>> > the HTML version of the relax manual, and not emails.  Run "relax -h"
>>> > to see a description of this option.
>>> >
>>> >
>>> > > Also, the reason its ./relax is because I have relax 2.2.5 installed,
>>> > and I
>>> > > have that set up as an Alias, so if I just type relax, it'll open up
>>> > relax
>>> > > 2.2.5. So I went to the actual relax-4.0.2. directory instead of
>>> > indicating
>>> > > its path and just typed ./relax. (By I, I mean the administrator of
>>> this
>>> > > computer, I do not have root access to this computer).
>>> >
>>> > You should set your alias to the relax-4.0.2 version instead.  The
>>> > 2.2.5 version is very, very old, and many bugs have been fixed since
>>> > then.
>>> >
>>> > Regards,
>>> >
>>> > Edward
>>> >
>>> ___
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>>>
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>>
>>
>
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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 19:47, Mahdi, Sam  wrote:
> I get the same results with the full path mpirun -np 5 ~/relax-4.0.2/relax
> --multi="mpi4py" -v
> Still no output.

The reason is because either OpenMPI or mpi4py are not working.  If
you compiled OpenMPI, then you'll have to compile mpi4py against that
self-compiled version of MPI.  Having multiple versions of MPI on the
system might be problematic, unless you know how to set your
environmental variables correctly for compilation and linking.  If you
cannot run the mpi4py demo that comes with the mpi4py source code,
then you do not have it set up correctly.  If you need help setting up
mpi4py for Python, please see the "Discussion and Support" section at
https://pythonhosted.org/mpi4py/ .  I don't think anyone on the relax
mailing lists have experience with broken mpi4py installations and can
help you fix this.

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Mahdi, Sam]

Sorry, I just want to make sure I fully understand this so I can explain it
to my PI:
So if there is symmetry, I can upload the same pdb file with the dimer (set
A and B) but tell it to read only one set. Since S^2 isn't effected too
much versus a dimer versus a monomer, the only thing that is important is
the change in co-ordinates of one set of the dimer (i.e. the differnence in
co-ordinates between set A in a monomer, and set A in a dimer co-ordinates,
or set A in a different version of that dimer's co-ordinates). I say this
because I have already run my protein's data with the pdb structure of the
monomer, and I have 2 different pdb files the docking program gave back for
the dimer (2 different ways the dimer could form from one interface).

Sincerely,
Sam

On Fri, Sep 30, 2016 at 10:29 AM, Edward d'Auvergne 
wrote:

> Hi Sam,
>
> Please see below:
>
> > I'm a bit confused to that. If the protein is a dimer, and the tumbling
> > decreases, will that not results in altered  relaxation data?
>
> Yes.
>
> > Won't the
> > relaxation data average be higher, since it is relaxing slower due to its
> > increased size (tumbler slower in solution=slower relaxation back to
> > equilibrium)?
>
> No.  R2 will be higher.  R1 could go anywhere.  The NOE may not be
> affected too much, but it may decrease (maybe).  You need to
> understand how the diffusion tensor affects the J(w) spectral density
> curves to understand how R1 and the NOE will be affected.
>
>
> > Also, doesn't S^2 take into account the overall shape of the
> > molecule (as well as tensor type) in it's calculations?
>
> No.  The S2 value is the internal motions of the residue.  It is 100%
> independent of the global tumbling.
>
>
> > So won't a dimer
> > versus a monomer change the results just due to that?
>
> Not at all.  The optimised diffusion tensor should change, and the S2
> value stay the same.
>
>
> > So should I input both, read_mol=0 and read_mol=1?
>
> No, only one.  You can, however, perform a second analysis later with
> read_mol=1 (for comparison).
>
>
> > So
> > structure.read_pdb(file='cluster1_12.pdb', dir=None,
> >  read_mol=None, set_mol_name='hRGS4',
> > read_model=None,set_model_num=0,set_mol_num=1, alt_loc=None,
> verbosity=1,
> > merge=False)
> > So mol_num=0 will be for chain A and mol_num=1 for chain B?
>
> This will have the same IndexError as before - relax will not handle
> two identical molecules in a model-free analysis at the same time.
> Again, this theory simply does not exist.  So I haven't added it to
> relax.  You need to perform the analysis on a single monomer of the
> homodimer.  But please check for symmetry - if you don't have
> symmetry, nobody on the planet can currently analyse non-symmetric
> homodimer data.
>
> Regards,
>
> Edward
>
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Re: Using multi-processor for model_free

[Troels Emtekær Linnet]

Sam.

All points to:
"./relax"   is NOT calling relax in the current folder.

It is because the command "mpirun" is running it.

Please provide the FULL path to relax.

I think I have written this before. ;)

Best
Troels


2016-09-30 19:24 GMT+02:00 Mahdi, Sam :

> Sorry, you're right, I re-ran the mpirun -np 5 ./relax --multi="mpi4py" -v
> and got no output. So I'm just curious for the other computers I download
> openmpi in, just installing it and compiling it isn't enough? There are
> some configurations you have to make to have it run on relax?
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne 
> wrote:
>
> > On 30 September 2016 at 19:12, Mahdi, Sam 
> > wrote:
> > > Hi Edward,
> > >
> > > So I ran the the mpirun commands you suggested. The echo world works
> > fine. I
> > > get the same results you did. For the relax one, this is the output I
> > > recieved
> > >  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax 4.0.2
> > > Usage: relax [options] [script_file]
> > >
> > > RelaxError: incorrect number of arguments
> >
> > Have a close look at my original text:
> >
> > [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
> > --multi="mpi4py" -v
> > relax 4.0.2
> > [edward@localhost ~]$
> >
> > Note how "relax 4.0.2" is on a different line - that is the relax
> > output, not the command line input.  Try again without that text.
> >
> >
> > > RelaxError: ambiguous option: --v (--verification-tests, --version?)
> >
> > This is because the double-dash to single-dash conversion is only in
> > the HTML version of the relax manual, and not emails.  Run "relax -h"
> > to see a description of this option.
> >
> >
> > > Also, the reason its ./relax is because I have relax 2.2.5 installed,
> > and I
> > > have that set up as an Alias, so if I just type relax, it'll open up
> > relax
> > > 2.2.5. So I went to the actual relax-4.0.2. directory instead of
> > indicating
> > > its path and just typed ./relax. (By I, I mean the administrator of
> this
> > > computer, I do not have root access to this computer).
> >
> > You should set your alias to the relax-4.0.2 version instead.  The
> > 2.2.5 version is very, very old, and many bugs have been fixed since
> > then.
> >
> > Regards,
> >
> > Edward
> >
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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

Hi Sam,

Please see below:

> I'm a bit confused to that. If the protein is a dimer, and the tumbling
> decreases, will that not results in altered  relaxation data?

Yes.

> Won't the
> relaxation data average be higher, since it is relaxing slower due to its
> increased size (tumbler slower in solution=slower relaxation back to
> equilibrium)?

No.  R2 will be higher.  R1 could go anywhere.  The NOE may not be
affected too much, but it may decrease (maybe).  You need to
understand how the diffusion tensor affects the J(w) spectral density
curves to understand how R1 and the NOE will be affected.


> Also, doesn't S^2 take into account the overall shape of the
> molecule (as well as tensor type) in it's calculations?

No.  The S2 value is the internal motions of the residue.  It is 100%
independent of the global tumbling.


> So won't a dimer
> versus a monomer change the results just due to that?

Not at all.  The optimised diffusion tensor should change, and the S2
value stay the same.


> So should I input both, read_mol=0 and read_mol=1?

No, only one.  You can, however, perform a second analysis later with
read_mol=1 (for comparison).


> So
> structure.read_pdb(file='cluster1_12.pdb', dir=None,
>  read_mol=None, set_mol_name='hRGS4',
> read_model=None,set_model_num=0,set_mol_num=1, alt_loc=None, verbosity=1,
> merge=False)
> So mol_num=0 will be for chain A and mol_num=1 for chain B?

This will have the same IndexError as before - relax will not handle
two identical molecules in a model-free analysis at the same time.
Again, this theory simply does not exist.  So I haven't added it to
relax.  You need to perform the analysis on a single monomer of the
homodimer.  But please check for symmetry - if you don't have
symmetry, nobody on the planet can currently analyse non-symmetric
homodimer data.

Regards,

Edward

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Re: Using multi-processor for model_free

[Mahdi, Sam]

Sorry, you're right, I re-ran the mpirun -np 5 ./relax --multi="mpi4py" -v
and got no output. So I'm just curious for the other computers I download
openmpi in, just installing it and compiling it isn't enough? There are
some configurations you have to make to have it run on relax?

Sincerely,
Sam

On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne 
wrote:

> On 30 September 2016 at 19:12, Mahdi, Sam 
> wrote:
> > Hi Edward,
> >
> > So I ran the the mpirun commands you suggested. The echo world works
> fine. I
> > get the same results you did. For the relax one, this is the output I
> > recieved
> >  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax 4.0.2
> > Usage: relax [options] [script_file]
> >
> > RelaxError: incorrect number of arguments
>
> Have a close look at my original text:
>
> [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
> --multi="mpi4py" -v
> relax 4.0.2
> [edward@localhost ~]$
>
> Note how "relax 4.0.2" is on a different line - that is the relax
> output, not the command line input.  Try again without that text.
>
>
> > RelaxError: ambiguous option: --v (--verification-tests, --version?)
>
> This is because the double-dash to single-dash conversion is only in
> the HTML version of the relax manual, and not emails.  Run "relax -h"
> to see a description of this option.
>
>
> > Also, the reason its ./relax is because I have relax 2.2.5 installed,
> and I
> > have that set up as an Alias, so if I just type relax, it'll open up
> relax
> > 2.2.5. So I went to the actual relax-4.0.2. directory instead of
> indicating
> > its path and just typed ./relax. (By I, I mean the administrator of this
> > computer, I do not have root access to this computer).
>
> You should set your alias to the relax-4.0.2 version instead.  The
> 2.2.5 version is very, very old, and many bugs have been fixed since
> then.
>
> Regards,
>
> Edward
>
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Re: relax-users Digest, Vol 116, Issue 38

[Mahdi, Sam]

Hi Edward,

I'm a bit confused to that. If the protein is a dimer, and the tumbling
decreases, will that not results in altered  relaxation data? Won't the
relaxation data average be higher, since it is relaxing slower due to its
increased size (tumbler slower in solution=slower relaxation back to
equilibrium)? Also, doesn't S^2 take into account the overall shape of the
molecule (as well as tensor type) in it's calculations? So won't a dimer
versus a monomer change the results just due to that?
So should I input both, read_mol=0 and read_mol=1? So
structure.read_pdb(file='cluster1_12.pdb', dir=None,
 read_mol=None, set_mol_name='hRGS4',
read_model=None,set_model_num=0,set_mol_num=1, alt_loc=None, verbosity=1,
merge=False)
So mol_num=0 will be for chain A and mol_num=1 for chain B?

Sincerely,
Sam

On Fri, Sep 30, 2016 at 9:17 AM, Edward d'Auvergne 
wrote:

> On 30 September 2016 at 17:31, Mahdi, Sam 
> wrote:
> > Hi Gary,
> >
> > There is only a monomer version of it on pdb, so if you mean it in that
> > sense, yes. I obtained results from it; however the S^2 were very high,
> but
> > I attributed this to having data for a dimer, but using a monomer pdb
> file.
>
> Hi Sam,
>
> This cannot be the case.  The S2 values are often very similar in a
> monomer and homodimer case.  Or a trimer, tetramer, etc.  The only
> difference is that the global tumbling - the diffusion tensor - is
> slower in the dimer/trimer/tetramer/etc. (and the tensor type and
> shape will be different due to the different hydrodynamic+water shell
> shape).
>
>
> > If you mean have I tried to just delete set B from the pdb file I
> uploaded,
> > I have not attempted that.
>
> With relax, you should never modify the PDB files - relax can do that
> for you much better and to the PDB standard via the PDB user
> functions.
>
>
> > So I am a bit confused here, so if I add read_mol=1 instead of my
> > read_mol=0, it'll only read set A?
>
> Sorry, I meant "read_mol=0" for PDB chain ID A.  The argument
> read_mol=1 will pull out chain ID B.
>
>
> > Assuming symmetry, relax will
> > automatically calculate and determine set B?
>
> Assuming symmetry, you will get the identical results for read_mol=0
> and read_mol=1.  There might be slight differences in bond orientation
> if the symmetry is not perfect.
>
> If there is no symmetry, the relaxation data for monomer A and monomer
> B will be different, but it will be averaged to a single value.  If
> this is the case, as I said before there is no theory on the planet
> for properly handling such averaged data, and you cannot perform any
> model-free, reduced spectral density mapping (J(w) mapping), or other
> analysis on it.
>
> I hope this clarifies the situation a little better.
>
> Regards,
>
> Edward
>
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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 19:12, Mahdi, Sam  wrote:
> Hi Edward,
>
> So I ran the the mpirun commands you suggested. The echo world works fine. I
> get the same results you did. For the relax one, this is the output I
> recieved
>  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax 4.0.2
> Usage: relax [options] [script_file]
>
> RelaxError: incorrect number of arguments

Have a close look at my original text:

[edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
--multi="mpi4py" -v
relax 4.0.2
[edward@localhost ~]$

Note how "relax 4.0.2" is on a different line - that is the relax
output, not the command line input.  Try again without that text.


> RelaxError: ambiguous option: --v (--verification-tests, --version?)

This is because the double-dash to single-dash conversion is only in
the HTML version of the relax manual, and not emails.  Run "relax -h"
to see a description of this option.


> Also, the reason its ./relax is because I have relax 2.2.5 installed, and I
> have that set up as an Alias, so if I just type relax, it'll open up relax
> 2.2.5. So I went to the actual relax-4.0.2. directory instead of indicating
> its path and just typed ./relax. (By I, I mean the administrator of this
> computer, I do not have root access to this computer).

You should set your alias to the relax-4.0.2 version instead.  The
2.2.5 version is very, very old, and many bugs have been fixed since
then.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 19:03, Mahdi, Sam  wrote:
> Hi Edward,
>
> So the GUI problems came from relax 2.2.5 The actual output is big, so I
> will only post where the errors started
> relax> monte_carlo.error_analysis()
>
> relax> results.write(file='devnull', dir='pipe_name', compress_type=1,
> force=True)
> Opening the null device file for writing.
> Traceback (most recent call last):

[snip]

> "/usr/local/Relax/relax-2.2.5/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py",
> line 121, in 
> print("A:\n" % cdp.align_tensors[0])
> TypeError: not all arguments converted during string formatting

[snip]

> That was for relax 2.2.5

These issues were fixed a long, long time ago ;)


> This is the output for relax 4.0.2 It seemed to run and finish, but it gave
> a bunch of errors that stated
> (python:28738): IBUS-WARNING **: Create input context failed: Timeout was
> reached.
>
> This warning basically takes up the entire terminal. Followed by this

These issues are with your Ibus input system, which I guess you have
set up for a few Indian languages on top of English, interacting with
wxPython (again a Fedora configuration issue).  Those are wxPython
messages which are not related to relax.  You should run the wxPython
demos and see if you can type with different Ibus languages, and see
if you get these same Ibus warnings.  No need to report back here
about that though - it would be of more benefit to report this
upstream to Fedora.

Regards,

Edward

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Re: Using multi-processor for model_free

[Mahdi, Sam]

Hi Edward,

So the GUI problems came from relax 2.2.5 The actual output is big, so I
will only post where the errors started
relax> monte_carlo.error_analysis()

relax> results.write(file='devnull', dir='pipe_name', compress_type=1,
force=True)
Opening the null device file for writing.
Traceback (most recent call last):
  File
"/usr/local/Relax/relax-2.2.5/test_suite/system_tests/n_state_model.py",
line 733, in test_paramag_centre_fit
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'paramag_centre_fit.py')
  File
"/usr/local/Relax/relax-2.2.5/test_suite/system_tests/base_classes.py",
line 65, in script_exec
self.interpreter.run(script_file=script)
  File "/usr/local/Relax/relax-2.2.5/prompt/interpreter.py", line 278, in
run
return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
  File "/usr/local/Relax/relax-2.2.5/prompt/interpreter.py", line 585, in
run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
  File "/usr/local/Relax/relax-2.2.5/prompt/interpreter.py", line 468, in
interact_script
exec_script(script_file, local)
  File "/usr/local/Relax/relax-2.2.5/prompt/interpreter.py", line 341, in
exec_script
runpy.run_module(module, globals)
  File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
fname, loader, pkg_name)
  File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
  File
"/usr/local/Relax/relax-2.2.5/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py",
line 121, in 
print("A:\n" % cdp.align_tensors[0])
TypeError: not all arguments converted during string formatting

--
Ran 284 tests in 279.175s

FAILED (errors=1)
##
# Unit tests #
##


.E.EE...E
==
ERROR: test_read_protein_noe_data
(test_suite.unit_tests._generic_fns.test_sequence.Test_sequence)
Test the reading of the amino acid sequence out of a protein NOE data file.
--
Traceback (most recent call last):
  File
"/usr/local/Relax/relax-2.2.5/test_suite/unit_tests/sequence_testing_base.py",
line 130, in test_read_protein_noe_data
self.sequence_fns.read(file='Ap4Aase.Noe.600.bz2',
dir=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'relaxation_data',
res_num_col=1, res_name_col=2)
  File "/usr/local/Relax/relax-2.2.5/generic_fns/sequence.py", line 339, in
read
for mol_name, res_num, res_name, spin_num, spin_name in
read_spin_data(file=file, dir=dir, file_data=file_data,
spin_id_col=spin_id_col, mol_name_col=mol_name_col,
res_num_col=res_num_col, res_name_col=res_name_col,
spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep,
spin_id=spin_id):
  File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 533, in
read_spin_data
file_data = extract_data(file, dir)
  File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 141, in extract_data
file = open_read_file(file_name=file, dir=dir)
  File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 345, in
open_read_file
compress_type, file_path = determine_compression(file_path)
  File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 112, in
determine_compression
raise RelaxFileError(file_path)
RelaxFileError: RelaxError: The file
'/usr/local/Relax/relax-2.2.5/test_suite/shared_data/relaxation_data/Ap4Aase.Noe.600.bz2'
does not exist.

Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 17:37, Mahdi, Sam  wrote:
> Hi Edward,
>
> I also wanted to add, for running a multi-processor platform problem. I
> installed openmpi from the fedora package list, not from the site itself. I
> installed both openmpi, mpi4py, and the openmpi devel. I did not modify
> anything. I can also successfully open relax using mpirun in a single
> processor mode (as in I can load the module, and do mpirun relax and it'll
> work). Do I actually have to do some modifications to openmpi for relax? The
> other computer I was able to successfully run multi-processor on, already
> had openmpi installed and set up, so I only downloaded mpi4py on that
> computer. So I don't know what their setting or configuration was.

Hi Sam,

This sounds like a Fedora OpenMPI misconfiguration.  I guess on the
computer that you see no output with relax, you would also see no
output with:

[edward@localhost ~]$ mpirun -np 5 echo "hello"
hello
hello
hello
hello
hello
[edward@localhost ~]$

In any case, this has nothing to do with relax.  And without a local
login to your computer, there is not much anyone can do about it.  Do
you have a system administrator there who can help you?  Oh, another
good and quick test is:

[edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
--multi="mpi4py" -v
relax 4.0.2
[edward@localhost ~]$

You should only see a single version number printed.  This tests both
your OpenMPI configuration and the mpi4py Python package.  If you do
not see these exact same results, you have some configuration work in
front of you ;)

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Mahdi, Sam]

Hi Gary,

There is only a monomer version of it on pdb, so if you mean it in that
sense, yes. I obtained results from it; however the S^2 were very high, but
I attributed this to having data for a dimer, but using a monomer pdb file.
If you mean have I tried to just delete set B from the pdb file I uploaded,
I have not attempted that.
So I am a bit confused here, so if I add read_mol=1 instead of my
read_mol=0, it'll only read set A? Assuming symmetry, relax will
automatically calculate and determine set B?

Sincerely,
Sam

On Fri, Sep 30, 2016 at 1:26 AM, Edward d'Auvergne 
wrote:

> On 30 September 2016 at 10:16, Edward d'Auvergne 
> wrote:
> > On 29 September 2016 at 09:55, Gary Thompson 
> wrote:
> >> Hi Sam
> >>
> >> have you tried with only one set of coordinates (i presume these are
> both homo dimers with some form of symetry plane or axis?
> >
> > Looking at the file attached to https://gna.org/bugs/?25133, the
> > problem is at the start of the script:
> >
> > """
> > relax> structure.read_pdb(file='cluster1_12.pdb', dir=None,
> > read_mol=None, set_mol_name='hRGS4', read_model=None,
> > set_model_num=None, alt_loc=None, verbosity=1, merge=False)
> >
> > Internal relax PDB parser.
> > Opening the file 'cluster1_12.pdb' for reading.
> > Adding molecule 'hRGS4' (from the original molecule number 1).
> > Merging with molecule 'hRGS4' (from the original molecule number 2).
> > """
> >
> > Note the text "Merging".  This is because you are setting all
> > molecules in the PDB file to the single molecule name "hRGS4".  What
> > you need to do is read a single molecule (via the 'read_mol'
> > argument).  Note Gary's text about symmetry.  If you have a homo dimer
> > without symmetry, there is absolutely no theory on the planet
> > currently developed to handle relaxation data in this situation.
>
> Running the RGS4_modelfree_sample_script.py script with the
> "read_mol=1" argument for the structure.read_pdb user function causes
> the IndexError to go away.  Unfortunately I don't have the time to
> investigate and turn this into a self-explanatory check and RelaxError
> yet.
>
> Cheers,
>
> Edward
>
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Re: Using multi-processor for model_free

[Mahdi, Sam]

Hi Edward,

I also wanted to add, for running a multi-processor platform problem. I
installed openmpi from the fedora package list, not from the site itself. I
installed both openmpi, mpi4py, and the openmpi devel. I did not modify
anything. I can also successfully open relax using mpirun in a single
processor mode (as in I can load the module, and do mpirun relax and it'll
work). Do I actually have to do some modifications to openmpi for relax?
The other computer I was able to successfully run multi-processor on,
already had openmpi installed and set up, so I only downloaded mpi4py on
that computer. So I don't know what their setting or configuration was.

Sincerely,
Sam

On Fri, Sep 30, 2016 at 8:22 AM, Mahdi, Sam 
wrote:

> Hi Edward,
>
> I have uploaded a bug with the pdb file, the relax data, and the script as
> well. I can upload the original pdb file I recieved from HADDOCK (without
> changing the HN to H). I will attempt to re-run my data again then on both
> computer. Most of the data was the same, but there were some data in from
> one computer, that was virtually non-existent in the other. Also to the
> relax -x error, I believe that was on the relax 2.5 version. I am
> re-running it on the 4.0.2. version.
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 12:04 AM, Edward d'Auvergne 
> wrote:
>
>> On 29 September 2016 at 00:23, Mahdi, Sam 
>> wrote:
>> > Hi Troels,
>> > Update on both proteins: So for protein 1, I can upload all the spins (H
>> > and N), but then I recieve an error. This is the error I recieved for
>> > protein 2 as well. These are both dimer pdb files. Meaning they have 2
>> sets
>> > (set A) and set (B) (e.g.
>> > http://www.rcsb.org/pdb/explore/explore.do?structureId=1DJ8 this pdb
>> > protein has 4 sets, A,B,C, and D ours only have A and B). For both these
>> > proteins I recieve this error
>> >  File "/home/crowlab/relax-4.0.2/multi/processor.py", line 494, in run
>> > self.callback.init_master(self)
>> >   File "/home/crowlab/relax-4.0.2/multi/__init__.py", line 318, in
>> > default_init_master
>> > self.master.run()
>> >   File "/home/crowlab/relax-4.0.2/relax.py", line 199, in run
>> > self.interpreter.run(self.script_file)
>> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 279, in
>> run
>> > return run_script(intro=self.__intro_string, local=locals(),
>> > script_file=script_file, show_script=self.__show_script,
>> > raise_relax_error=self.__raise_relax_error)
>> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 585, in
>> > run_script
>> > return console.interact(intro, local, script_file,
>> > show_script=show_script, raise_relax_error=raise_relax_error)
>> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 484, in
>> > interact_script
>> > exec_script(script_file, local)
>> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 363, in
>> > exec_script
>> > runpy.run_module(module, globals)
>> >   File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
>> > fname, loader, pkg_name)
>> >   File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
>> > exec code in run_globals
>> >   File "/home/crowlab/relax-4.0.2/RGS4_modelfree_sample_script.py",
>> line
>> > 31, in 
>> >
>> > dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di
>> ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=
>> LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_
>> sim_num=MC_NUM,conv_loop=CONV_LOOP)
>> >   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>> > line 246, in __init__
>> > self.execute()
>> >   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>> > line 600, in execute
>> > self.multi_model(local_tm=True)
>> >   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>> > line 888, in multi_model
>> > self.interpreter.minimise.grid_search(inc=self.grid_inc)
>> >   File "/home/crowlab/relax-4.0.2/prompt/uf_objects.py", line 225, in
>> > __call__
>> > self._backend(*new_args, **uf_kargs)
>> >   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 172,
>> in
>> > grid_search
>> > model_lower, model_upper, model_inc = grid_setup(lower, upper, inc,
>> > verbosity=verbosity, skip_preset=skip_preset)
>> >   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 341,
>> in
>> > grid_setup
>> > elif values[i] in [None, {}, []]:
>> > IndexError: index out of bounds
>> >
>> > Which from my understanding basically means, the co-ordinates of the
>> spins
>> > are out of the acceptable range for relax. I've checked all the
>> > co-ordinates for both, nothing is extreme or outlandish (all within a
>> range
>> > of -20 to 20).
>> > Is relax unable to process pdb files that are dimers (with 2 sets A and
>> > B).? Furthermore, is it unable to process trimers and tetramers?
>>
>> Hi,
>>
>> For the model-free 

Re: Using multi-processor for model_free

[Mahdi, Sam]

Hi Edward,

I have uploaded a bug with the pdb file, the relax data, and the script as
well. I can upload the original pdb file I recieved from HADDOCK (without
changing the HN to H). I will attempt to re-run my data again then on both
computer. Most of the data was the same, but there were some data in from
one computer, that was virtually non-existent in the other. Also to the
relax -x error, I believe that was on the relax 2.5 version. I am
re-running it on the 4.0.2. version.

Sincerely,
Sam

On Fri, Sep 30, 2016 at 12:04 AM, Edward d'Auvergne 
wrote:

> On 29 September 2016 at 00:23, Mahdi, Sam 
> wrote:
> > Hi Troels,
> > Update on both proteins: So for protein 1, I can upload all the spins (H
> > and N), but then I recieve an error. This is the error I recieved for
> > protein 2 as well. These are both dimer pdb files. Meaning they have 2
> sets
> > (set A) and set (B) (e.g.
> > http://www.rcsb.org/pdb/explore/explore.do?structureId=1DJ8 this pdb
> > protein has 4 sets, A,B,C, and D ours only have A and B). For both these
> > proteins I recieve this error
> >  File "/home/crowlab/relax-4.0.2/multi/processor.py", line 494, in run
> > self.callback.init_master(self)
> >   File "/home/crowlab/relax-4.0.2/multi/__init__.py", line 318, in
> > default_init_master
> > self.master.run()
> >   File "/home/crowlab/relax-4.0.2/relax.py", line 199, in run
> > self.interpreter.run(self.script_file)
> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 279, in
> run
> > return run_script(intro=self.__intro_string, local=locals(),
> > script_file=script_file, show_script=self.__show_script,
> > raise_relax_error=self.__raise_relax_error)
> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 585, in
> > run_script
> > return console.interact(intro, local, script_file,
> > show_script=show_script, raise_relax_error=raise_relax_error)
> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 484, in
> > interact_script
> > exec_script(script_file, local)
> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 363, in
> > exec_script
> > runpy.run_module(module, globals)
> >   File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
> > fname, loader, pkg_name)
> >   File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
> > exec code in run_globals
> >   File "/home/crowlab/relax-4.0.2/RGS4_modelfree_sample_script.py", line
> > 31, in 
> >
> > dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,
> diff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_
> models=LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_
> ALGOR,mc_sim_num=MC_NUM,conv_loop=CONV_LOOP)
> >   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> > line 246, in __init__
> > self.execute()
> >   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> > line 600, in execute
> > self.multi_model(local_tm=True)
> >   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> > line 888, in multi_model
> > self.interpreter.minimise.grid_search(inc=self.grid_inc)
> >   File "/home/crowlab/relax-4.0.2/prompt/uf_objects.py", line 225, in
> > __call__
> > self._backend(*new_args, **uf_kargs)
> >   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 172,
> in
> > grid_search
> > model_lower, model_upper, model_inc = grid_setup(lower, upper, inc,
> > verbosity=verbosity, skip_preset=skip_preset)
> >   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 341,
> in
> > grid_setup
> > elif values[i] in [None, {}, []]:
> > IndexError: index out of bounds
> >
> > Which from my understanding basically means, the co-ordinates of the
> spins
> > are out of the acceptable range for relax. I've checked all the
> > co-ordinates for both, nothing is extreme or outlandish (all within a
> range
> > of -20 to 20).
> > Is relax unable to process pdb files that are dimers (with 2 sets A and
> > B).? Furthermore, is it unable to process trimers and tetramers?
>
> Hi,
>
> For the model-free analysis in relax, as well as all other analyses,
> we have designed the program to try to catch all user input errors and
> to produce a specific RelaxError prior to minimisation explaining
> exactly what went wrong.  An IndexError here simply shows that not all
> erroneous data input has been caught.  Let me go back to your PDB
> file.  You should not edit this file unless you know exactly what you
> are doing, but relax will handle all PDB files.  There is no need to
> rename protons.  You just specify the correct proton name in the input
> script.  I may have missed it as there is a lot of correspondence I
> have to catch up on, but did you upload your script and a truncated
> set of data to the relax bug or support trackers?  Do you have a
> mini-data set (1 or 2 residues) and script that triggers this error?
> If we can reproduce the IndexError, then 

Re: Issue in ModelFree Calculation

[Edward d'Auvergne]

On 26 August 2016 at 18:25,   wrote:
> Hi Edward,
> Thank you for your suggestions. Extremely sorry for my late reply. I already
> tried what Troel had told me. As I didn't install the SciPy package (not
> required for ModelFree analysis), I am unable to perform the full test
> suite. As per your suggestion, I went through the wxPython demo, and found a
> missing link of a library package which I have successfully rebuild. Now
> wxPython is setup correctly. But still I get the same error like previous:
>
> terminate called after throwing an instance of 'std::bad_alloc'
>   what():  std::bad_alloc
> Abort (core dumped)
>
> This time I didn't get errors with the libraries. I have also attached the
> output of "$relax -i". Kindly suggest something to resolve this problem.

Hi Aritra,

Did you work out how to correctly install wxPython in the end?  I have
never seen this std::bad_alloc when using different wxPython versions
for almost a decade, so I cannot really help you debug your private
wxPython software installation.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 01:35, Mahdi, Sam  wrote:
> Also, Congrats to Edward!

Thanks :)

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 28 September 2016 at 22:44, Mahdi, Sam  wrote:
> Hey Troels,
>
> I ran the relax -x and recieve this error at the GUI tests
> =
> = GUI tests =
> =
>
> **
> Gtk:ERROR:gtkfilesystemmodel.c:746:gtk_file_system_model_sort: assertion
> failed: (r == n_visible_rows)
> Abort (core dumped)
> crowlab: [~/relax-4.0.2]>

That is a strange error, but it shouldn't effect you.  It is a minor
problem with your wxPython setup and GTK+ on your system.  It's only
an issue if you are running the GUI and the GUI suddenly crashes on
you.  But again, this problem is not due to relax.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 28 September 2016 at 20:32, Troels Emtekær Linnet
 wrote:
> If you get different results, for the same setup, this is not good.
> Not at all !

Hi,

Sorry for not being more involved, I've been in what could be called
paternity leave.  This point is very, very important.  With the same
setup you must absolutely always obtain the same result.  There are
numerical precision differences between operating systems, CPU types,
and Python 2 vs. 3, but this should be very small.

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 33

[Gary Thompson]

Hi Sam 

if you log to file, tail -f of the log file gives a good overview of the output 
and minimisation without the overhead



regards
gary
-- 
---
Dr Gary Thompson[Leeds Biological NMR Facility]

Astbury Centre for Structural Molecular Biology,
University of Leeds,
Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
email: ga...@bmb.leeds.ac.uk   Fax  +44-113-3431935
---



> On 28 Sep 2016, at 19:27, relax-users-requ...@gna.org wrote:
> 
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> Today's Topics:
> 
>   1. Re: Using multi-processor for model_free (Troels Emtekær Linnet)
> 
> 
> --
> 
> Message: 1
> Date: Wed, 28 Sep 2016 20:26:59 +0200
> From: Troels Emtekær Linnet 
> To: "Mahdi, Sam" 
> Cc: "relax-users@gna.org" 
> Subject: Re: Using multi-processor for model_free
> Message-ID:
>   
> Content-Type: text/plain; charset=UTF-8
> 
> Another possibility for the "slowness" is "the very well known" that,
> printing to screen makes
> python slow.
> 
> Extremely slow...
> 
> And all the minimization information to screen actually slow downs relax
> (through python).
> 
> For even faster calculations, just "log" the relax output with -l, and do
> not "tee" -t and print to screen.
> Try skipping all printing to screen.
> 
> You lose the ability to follow the process live, but you win in speed !
> 
> A possible explanation for the slow GUI, is that printing to screen through
> the GUI is a terrible process.
> Try to imagine how many "computer layers" the "text" has to travel through,
> to arrive in the "GUI screen".
> The worst is, it is almost impossible to "really" test.
> 
> 
> 
> 
> 
> 
> 
> 2016-09-28 9:44 GMT+02:00 Mahdi, Sam :
> 
>> Hi Troels,
>> 
>> I wanted to give a bit of feedback on the results I've obtained throughout
>> the few weeks I've been using model free on relax. First off, thank you
>> guys (both you and Edward) immensly for your patience and help as I
>> attempted to understand and work relax. Secondly, I have noticed a
>> difference between using the gui and the terminal (using scripts to run
>> relax). I've currently finished about 3 runs using the gui, and 3 runs
>> using the terminal (all the same data sets, same pdb files, same settings,
>> etc.). The gui takes about a week to finish, where the terminal takes
>> approximately 24 hours. I've tried this on 2 proteins, both had the same
>> results. The terminal is by far, much faster than the gui. Finally, I've
>> run 1 protein on 2 different computers (one using the multi-processor
>> platform, and on another computer, single-processor). The data sets were
>> all the same, the same pdb file, etc. , but the results I obtained from the
>> computers were slightly different. For the most part, most of the
>> difference in the data was similar, slightly different, but within the
>> error. But there were about 7 or 8 data points that appeared in one run on
>> one computer, and were absent in another run on another computer. This
>> happened in both the S^2 I analyzed and the Rex.
>> I.e. On the fedora 20 (single processor), say I had S^2 values for amino
>> acid 24,25 and 26 in the sequence, but not for 28,29, and 30. On the fedora
>> 24 (multi-processor), I might be missing a value for amino acid 24, but I
>> would have S^2 values for 28,29 and 30. Note the data sets are all the
>> same, the pdb files the same, settings the same, I used the same script for
>> both. The only difference between these runs is they were run on different
>> computer and one was single processor well another was multi.
>> I don't know why I obtained different data from 2 different runs, when the
>> input was all the same, just on different computers.
>> However the S^2 values do make sense. The Rex values were incredibly small
>> (1x10^-20), but there are some similarities (in terms of big Rex values)
>> between the Rex I obtained from relax, and CPMG data analyzed by glove. So
>> I have been able to obtain some reasonable data and results from model_free
>> using relax.
>> 
>> Sincerely,
>> Sam
>> 
>> 
>> 
>> On Mon, Sep 26, 2016 at 2:59 PM, Mahdi, Sam 
>> wrote:
>> 
>>> Hi 

Re: relax-users Digest, Vol 116, Issue 38

[Gary Thompson]

Hi Sam

have you tried with only one set of coordinates (i presume these are both homo 
dimers with some form of symetry plane or axis?

regards
gary
-- 
---
Dr Gary Thompson[Leeds Biological NMR Facility]

Astbury Centre for Structural Molecular Biology,
University of Leeds,
Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
email: ga...@bmb.leeds.ac.uk   Fax  +44-113-3431935
---



> On 28 Sep 2016, at 23:24, relax-users-requ...@gna.org wrote:
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> Today's Topics:
> 
>   1. Re: Using multi-processor for model_free (Mahdi, Sam)
> 
> 
> --
> 
> Message: 1
> Date: Wed, 28 Sep 2016 15:23:58 -0700
> From: "Mahdi, Sam" 
> To: Troels Emtekær Linnet ,
>   relax-users@gna.org
> Subject: Re: Using multi-processor for model_free
> Message-ID:
>   
> Content-Type: text/plain; charset=UTF-8
> 
> Hi Troels,
> Update on both proteins: So for protein 1, I can upload all the spins (H
> and N), but then I recieve an error. This is the error I recieved for
> protein 2 as well. These are both dimer pdb files. Meaning they have 2 sets
> (set A) and set (B) (e.g.
> http://www.rcsb.org/pdb/explore/explore.do?structureId=1DJ8 this pdb
> protein has 4 sets, A,B,C, and D ours only have A and B). For both these
> proteins I recieve this error
> File "/home/crowlab/relax-4.0.2/multi/processor.py", line 494, in run
>self.callback.init_master(self)
>  File "/home/crowlab/relax-4.0.2/multi/__init__.py", line 318, in
> default_init_master
>self.master.run()
>  File "/home/crowlab/relax-4.0.2/relax.py", line 199, in run
>self.interpreter.run(self.script_file)
>  File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 279, in run
>return run_script(intro=self.__intro_string, local=locals(),
> script_file=script_file, show_script=self.__show_script,
> raise_relax_error=self.__raise_relax_error)
>  File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 585, in
> run_script
>return console.interact(intro, local, script_file,
> show_script=show_script, raise_relax_error=raise_relax_error)
>  File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 484, in
> interact_script
>exec_script(script_file, local)
>  File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 363, in
> exec_script
>runpy.run_module(module, globals)
>  File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
>fname, loader, pkg_name)
>  File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
>exec code in run_globals
>  File "/home/crowlab/relax-4.0.2/RGS4_modelfree_sample_script.py", line
> 31, in 
> 
> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,diff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_num=MC_NUM,conv_loop=CONV_LOOP)
>  File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> line 246, in __init__
>self.execute()
>  File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> line 600, in execute
>self.multi_model(local_tm=True)
>  File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> line 888, in multi_model
>self.interpreter.minimise.grid_search(inc=self.grid_inc)
>  File "/home/crowlab/relax-4.0.2/prompt/uf_objects.py", line 225, in
> __call__
>self._backend(*new_args, **uf_kargs)
>  File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 172, in
> grid_search
>model_lower, model_upper, model_inc = grid_setup(lower, upper, inc,
> verbosity=verbosity, skip_preset=skip_preset)
>  File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 341, in
> grid_setup
>elif values[i] in [None, {}, []]:
> IndexError: index out of bounds
> 
> Which from my understanding basically means, the co-ordinates of the spins
> are out of the acceptable range for relax. I've checked all the
> co-ordinates for both, nothing is extreme or outlandish (all within a range
> of -20 to 20).
> Is relax unable to process pdb files that are dimers (with 2 sets A and
> B).? Furthermore, is it unable to process trimers and tetramers?
> 
> Sincerely,
> Sam
> 
> On Wed, Sep 28, 2016 at 1:44 PM, Mahdi, Sam