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List: relax-users
Subject: Re: Unselecting residues in full_analysis.py
From: Sébastien_Morin <sebastien.morin.1 () domain ! hid>
Date: 2008-05-31 21:14:17
Message-ID: 4841BFA9.90706 () domain ! hid
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Hi Ed,
This is exactly what I was thinking.
Thanks for translating my idea into something which can be implemented
into relax..!
Séb
Edward d'Auvergne wrote:
> Hi,
>
> This proposal could be quite useful, and simple to implement in the
> full_analysis.py script. I could add a variable called something like
> EXCLUDE which points to another file. This would then be used with
> the spin system deselection user function (unselect.read() in the 1.2
> line and deselect.read() in the 1.3 line). These would then not only
> be excluded in the multi_model() method of the script, but also in the
> 'init' round of optimisation to cover all places in the script. Then
> you could take any relax model-free results file as the input, and the
> spins in EXCLUDE will never be used in the analysis. Is this along
> the lines of what you were thinking? The UNRES file would still be
> there, but this would serve a different purpose than then EXCLUDE
> file.
>
> Regards,
>
> Edward
>
>
>
> On Tue, May 27, 2008 at 3:55 PM, Sébastien Morin
> <sebastien.morin.1@domain.hid> wrote:
>
>> Hi,
>>
>> First, thanks for answering this question.
>>
>> Here are some precisions...
>>
>> If one wants to analyze a protein and doesn't know much about the global
>> dynamics, the first step will probably be to make a full analysis on all
>> of the protein.
>>
>> Then, if that person thinks an hybrid would be better, tests could be
>> made excluding, let's say, the flexible C-terminus. To save time, one
>> could take advantage of the already minimized "local_tm" run... Hence,
>> this user could just exclude the C-terminus residues with the 'UNRES'
>> variable in the different scripts for the other different diffusion
>> tensor (but not the "local_tm" which is already available, even though
>> for more residues).
>>
>> So, my question was about knowing if initializing a diffusion tensor
>> with more residues would be bad. You answered yes, i.e. that one should
>> initialize diffusion tensors using only the wanted residues.
>>
>> So, would it be a good idea to add a variable in the full_analysis
>> script so a different 'UNRES' variable can be used for "local_tm" and
>> other diffusion tensors..? If a different 'UNRES' variable would be
>> used, the "init" run could only use the selected residues and exclude
>> others, even if they are present in the "local_tm" run... This would
>> allow one to skip the "local_tm" run when trying some hybrids... This
>> would save lots of time...
>>
>> What do you think of this proposal ? Is this useful ? Is this feasible ?
>>
>> Thanks !
>>
>>
>> Séb
>>
>>
>>
>>
>> Edward d'Auvergne wrote:
>>
>>> On Sun, May 11, 2008 at 10:33 PM, Sébastien Morin
>>> <sebastien.morin.1@domain.hid> wrote:
>>>
>>>
>>>> Hi,
>>>>
>>>> When using the full_analysis.py script, unselecting residues is possible
>>>> by inputing a list of residues under the variable name UNRES.
>>>>
>>>> Two approaches are possible.
>>>>
>>>> 1.
>>>> Excluding residues a priori.
>>>>
>>>> 2.
>>>> Excluding residues after an initial test where at least the local_tm run
>>>> as been completed. Let's say, for example, that one wants to produce an
>>>> hybrid after an initial test with all residues fitted together.
>>>>
>>>>
>>> Both are fine because the local tm models are completely independent
>>> of each other.
>>>
>>>
>>>
>>>
>>>> In situation 2, one may want to re-use the local_tm run and exclude
>>>> residues from there on (to save time). This works fine for subsequent
>>>> rounds for diffusion tensors sphere, prolate, oblate and ellipsoid.
>>>>
>>>> However, the "init" round (before round 1) still includes the residues
>>>> to be excluded, since those were present in the local_tm run.
>>>>
>>>> Is this a problem ? Will this presence of subsequently excluded residues
>>>> bias the diffusion tensor and avoid the user from finding the global
>>>> minimum ?
>>>>
>>>>
>>> This is a problem as the initial diffusion tensor optimisation should
>>> only include spins located within this isolated diffusion unit.
>>>
>>>
>>>
>>>
>>>> Should excluded residues be excluded from ALL the runs, including the
>>>> local_tm run (which serves for creating the "init" round of other runs) ?
>>>>
>>>>
>>> Well, that depends on why you are excluding them. If the relaxation
>>> data is rubbish, then these should be excluded everywhere. This is
>>> the case with the spin list in UNRES, and this will be propagated in
>>> full_analysis.py into the 'init' round of optimisation because of the
>>> loading of the local tm results file. For a hybrid model, this needs
>>> to be constructed differently. If you place the spins to exclude into
>>> the UNRES file, then these will be excluded in all parts of the
>>> full_analysis.py script.
>>>
>>> I hope this helps.
>>>
>>> Regards,
>>>
>>> Edward
>>>
>>>
>>>
>>
>
>
>
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Hi Ed,<br>
<br>
This is exactly what I was thinking.<br>
<br>
Thanks for translating my idea into something which can be implemented
into relax..!<br>
<br>
<br>
Séb<br>
<br>
<br>
<br>
<br>
Edward d'Auvergne wrote:
<blockquote
cite="mid:7f080ed10805280653g4d7c6730ic5afa5f08ebcc4aa@domain.hid.com"
type="cite">
<pre wrap="">Hi,
This proposal could be quite useful, and simple to implement in the
full_analysis.py script. I could add a variable called something like
EXCLUDE which points to another file. This would then be used with
the spin system deselection user function (unselect.read() in the 1.2
line and deselect.read() in the 1.3 line). These would then not only
be excluded in the multi_model() method of the script, but also in the
'init' round of optimisation to cover all places in the script. Then
you could take any relax model-free results file as the input, and the
spins in EXCLUDE will never be used in the analysis. Is this along
the lines of what you were thinking? The UNRES file would still be
there, but this would serve a different purpose than then EXCLUDE
file.
Regards,
Edward
On Tue, May 27, 2008 at 3:55 PM, Sébastien Morin
<a class="moz-txt-link-rfc2396E" \
href="mailto:sebastien.morin.1@domain.hidlaval.ca"><sebastien.morin.1@domain.hid></a> \
wrote: </pre>
<blockquote type="cite">
<pre wrap="">Hi,
First, thanks for answering this question.
Here are some precisions...
If one wants to analyze a protein and doesn't know much about the global
dynamics, the first step will probably be to make a full analysis on all
of the protein.
Then, if that person thinks an hybrid would be better, tests could be
made excluding, let's say, the flexible C-terminus. To save time, one
could take advantage of the already minimized "local_tm" run... Hence,
this user could just exclude the C-terminus residues with the 'UNRES'
variable in the different scripts for the other different diffusion
tensor (but not the "local_tm" which is already available, even though
for more residues).
So, my question was about knowing if initializing a diffusion tensor
with more residues would be bad. You answered yes, i.e. that one should
initialize diffusion tensors using only the wanted residues.
So, would it be a good idea to add a variable in the full_analysis
script so a different 'UNRES' variable can be used for "local_tm" and
other diffusion tensors..? If a different 'UNRES' variable would be
used, the "init" run could only use the selected residues and exclude
others, even if they are present in the "local_tm" run... This would
allow one to skip the "local_tm" run when trying some hybrids... This
would save lots of time...
What do you think of this proposal ? Is this useful ? Is this feasible ?
Thanks !
Séb
Edward d'Auvergne wrote:
</pre>
<blockquote type="cite">
<pre wrap="">On Sun, May 11, 2008 at 10:33 PM, Sébastien Morin
<a class="moz-txt-link-rfc2396E" \
href="mailto:sebastien.morin.1@domain.hidlaval.ca"><sebastien.morin.1@domain.hid></a> \
wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
When using the full_analysis.py script, unselecting residues is possible
by inputing a list of residues under the variable name UNRES.
Two approaches are possible.
1.
Excluding residues a priori.
2.
Excluding residues after an initial test where at least the local_tm run
as been completed. Let's say, for example, that one wants to produce an
hybrid after an initial test with all residues fitted together.
</pre>
</blockquote>
<pre wrap="">Both are fine because the local tm models are completely \
independent of each other.
</pre>
<blockquote type="cite">
<pre wrap="">In situation 2, one may want to re-use the local_tm run and \
exclude residues from there on (to save time). This works fine for subsequent
rounds for diffusion tensors sphere, prolate, oblate and ellipsoid.
However, the "init" round (before round 1) still includes the residues
to be excluded, since those were present in the local_tm run.
Is this a problem ? Will this presence of subsequently excluded residues
bias the diffusion tensor and avoid the user from finding the global
minimum ?
</pre>
</blockquote>
<pre wrap="">This is a problem as the initial diffusion tensor optimisation \
should only include spins located within this isolated diffusion unit.
</pre>
<blockquote type="cite">
<pre wrap="">Should excluded residues be excluded from ALL the runs, \
including the local_tm run (which serves for creating the "init" round of other runs) \
?
</pre>
</blockquote>
<pre wrap="">Well, that depends on why you are excluding them. If the \
relaxation data is rubbish, then these should be excluded everywhere. This is
the case with the spin list in UNRES, and this will be propagated in
full_analysis.py into the 'init' round of optimisation because of the
loading of the local tm results file. For a hybrid model, this needs
to be constructed differently. If you place the spins to exclude into
the UNRES file, then these will be excluded in all parts of the
full_analysis.py script.
I hope this helps.
Regards,
Edward
</pre>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
</blockquote>
<br>
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