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

[Edward d'Auvergne]

On 29 October 2016 at 23:44, Mahdi, Sam  wrote:
> Hi Edward,
>
> I was reading the theory on model free within the manual and I had a quick
> question. The d'Auvergne protocol, is that the model-free analysis in
> reverse with the universal solution?

Yes, that is the technique.

> Or is that the model-free models with
> only the AIC model selection (no universal solution). Both methods were
> under the new-protocol section, so I was confused a bit as to which one the
> d'Auvergne protocol is running.

This is a fragment of the protocol.  It is one part of the iterative
procedure shared with the methods that require an initial, external
diffusion tensor estimate.  The key references to understand all of
this are:

d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of
the model-free problem and the diffusion seeded model-free paradigm.
Mol. Biosyst., 3(7), 483-494. (http://dx.doi.org/10.1039/b702202f)

d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models II. A new methodology for the dual optimisation of the
model-free parameters and the Brownian rotational diffusion tensor. J.
Biomol. NMR, 40(2), 121-133.
(http://dx.doi.org/10.1007/s10858-007-9213-3)

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

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

[Edward d'Auvergne]

On 4 October 2016 at 23:23, Mahdi, Sam  wrote:
> Hi Edward,
>
> Just wanted to update you on the status of my runs. I had 2 potential dimer
> structures. I ran Chain A and B for one of them, and Chain B for the other.
> All the results were all very similar. There was missing data though
> throughout (i.e. I had data for some residues for Chain A that had no data
> in Chain B, Or chain A for one pdb file and Chain B for the other pdb file
> would have data, but Chain B for the other pdb file wouldn't). The data that
> is there for all 3 though does make sense. Thank you so much for your help

You're welcome!  Thanks too to Troels and Gary for answering most of
your questions.

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

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

[Mahdi, Sam]

Hi Edward,

Just wanted to update you on the status of my runs. I had 2 potential dimer
structures. I ran Chain A and B for one of them, and Chain B for the other.
All the results were all very similar. There was missing data though
throughout (i.e. I had data for some residues for Chain A that had no data
in Chain B, Or chain A for one pdb file and Chain B for the other pdb file
would have data, but Chain B for the other pdb file wouldn't). The data
that is there for all 3 though does make sense. Thank you so much for your
help

Sincerely,
Sam

On Sat, Oct 1, 2016 at 11:17 AM, Edward d'Auvergne 
wrote:

> On 1 October 2016 at 20:14, Mahdi, Sam  wrote:
> > Hi Edward,
> >
> > Oh ok. Thank you for your help, I was able to resolve the problems I had
> > with both proteins, and now they are both running. Since there is
> symmetry
> > within the dimer, both chain A and chain B will give me the same S^2
> results
> > correct?
>
> Hi Sam,
>
> That depends.  If you superimpose A and B and have an RMSD of
> 0.0, then the S2 values will be identical.  But if
> the docking software changed the monomer structures slightly so the
> RMSD is not exactly zero, then the S2 values will be slightly
> different for some residues.  You can use relax to superimpose
> structures and determine the RMSD to very high precision, if you like,
> but I'll leave that to you as a learning exercise ;)
>
> 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

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

[Edward d'Auvergne]

On 1 October 2016 at 20:14, Mahdi, Sam  wrote:
> Hi Edward,
>
> Oh ok. Thank you for your help, I was able to resolve the problems I had
> with both proteins, and now they are both running. Since there is symmetry
> within the dimer, both chain A and chain B will give me the same S^2 results
> correct?

Hi Sam,

That depends.  If you superimpose A and B and have an RMSD of
0.0, then the S2 values will be identical.  But if
the docking software changed the monomer structures slightly so the
RMSD is not exactly zero, then the S2 values will be slightly
different for some residues.  You can use relax to superimpose
structures and determine the RMSD to very high precision, if you like,
but I'll leave that to you as a learning exercise ;)

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

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

[Mahdi, Sam]

Hi Edward,

Oh ok. Thank you for your help, I was able to resolve the problems I had
with both proteins, and now they are both running. Since there is symmetry
within the dimer, both chain A and chain B will give me the same S^2
results correct?

Sincerely,
Sam

On Sat, Oct 1, 2016 at 2:21 AM, Edward d'Auvergne 
wrote:

> On 30 September 2016 at 23:42, Mahdi, Sam 
> wrote:
> > 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?
>
> Sorry, I just remembered that the molecule numbering starts from 1.
> So read_mol=1 gives chain ID A and read_mol=2 gives chain ID B.  I
> should add a check for this argument.
>
> 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

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

[Edward d'Auvergne]

On 30 September 2016 at 23:42, Mahdi, Sam  wrote:
> 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?

Sorry, I just remembered that the molecule numbering starts from 1.
So read_mol=1 gives chain ID A and read_mol=2 gives chain ID B.  I
should add a check for this argument.

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

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
>>
>
>
___
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 

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
>
___
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

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

___
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

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
>
___
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

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

___
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

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
>
___
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

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
>
> ___
> 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
>
___
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

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:
> 
> Send relax-users mailing list submissions to
>   relax-users@gna.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>   https://mail.gna.org/listinfo/relax-users
> or, via email, send a message with subject or body 'help' to
>   relax-users-requ...@gna.org
> 
> You can reach the person managing the list at
>   relax-users-ow...@gna.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of relax-users digest..."
> 
> 
> 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