'Re: The use of a pdb with the sphere diffusion tensor'

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List:       relax-users
Subject:    Re: The use of a pdb with the sphere diffusion tensor
From:       Sebastien Morin <sebastien.morin.1 () domain ! hid>
Date:       2008-01-10 21:44:05
Message-ID: 478691A5.5020908 () domain ! hid
[Download RAW message or body]

Hi,

You're right. Sorry for that... It is corrected in r4620.


Séb


Edward d'Auvergne wrote:
> Actually, the test you proposed:
>
> =============
>             # Unselect unresolved residues.
>             if not UNRES:
>                 unselect.read(name, file=UNRES)
> =============
>
> should not include not.  The statement needed is that if the UNRES
> file exists, use it to deselect the residues.  It currently say that
> if the UNRES file does not exist, use it to deselect the residues.
> Sorry, I should have seen that one.
>
> Regards,
>
> Edward
>
>
> On Jan 10, 2008 10:17 PM, Sebastien Morin <sebastien.morin.1@domain.hid> wrote:
>   
>>  I tried the line a you proposed :
>>
>>  UNRES = None
>>
>>  and it yields an error.
>>
>>  relax> unselect.read(run='tm0', file=None, dir=None, change_all=0,
>> column=0)
>>  RelaxError: The file name argument None must be a string.
>>
>>  However,
>>
>>  UNRES = 'None'
>>
>>  does not yield this error and the script proceeds...
>>
>>  Am I right ?
>>
>>
>>  Séb  :)
>>
>>
>>
>>
>>
>>
>>
>>  Edward d'Auvergne wrote:
>>  On Jan 10, 2008 9:59 PM, Sebastien Morin <sebastien.morin.1@domain.hid>
>> wrote:
>>
>>
>>  Thanks Ed !
>>
>>  Another similar would maybe ease life of users without PDB or with small
>> proteins... We could add the possibility of not having any file for
>> unresolved residues...
>>
>>  The lines :
>>  =============
>>  # The file containing the list of unresolved residues to exclude from the
>> analysis.
>>  UNRES = 'unresolved'
>>  =============
>>
>>  could become :
>>  =============
>>  # The file containing the list of unresolved residues to exclude from the
>> analysis (set this to None if no residue is to be excluded).
>>  UNRES = 'None'
>>  =============
>>
>>  This should be:
>>
>> UNRES = None
>>
>> rather than a string. The user will instantly see the problem if
>> 'None' is supplied as a string. But this is a good idea, so feel free
>> to make the changes. Don't forget to port the changes to the 1.3 line
>> using 'svn merge'.
>>
>> Regards,
>>
>> Edward
>>
>>
>>
>>
>> --
>> Sebastien Morin
>> Etudiant au PhD en biochimie
>> Laboratoire de resonance magnetique nucleaire
>> Dr Stephane Gagne
>> CREFSIP (Universite Laval, Quebec, CANADA)
>> 1-418-656-2131 #4530
>>
>>
>>     
>
>   

-- 
Sebastien Morin
Etudiant au PhD en biochimie
Laboratoire de resonance magnetique nucleaire
Dr Stephane Gagne
CREFSIP (Universite Laval, Quebec, CANADA)
1-418-656-2131 #4530


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Hi,<br>
<br>
You're right. Sorry for that... It is corrected in r4620.<br>
<br>
<br>
S&eacute;b<br>
<br>
<br>
Edward d'Auvergne wrote:
<blockquote
 cite="mid:7f080ed10801101337r590054f7mc9fca97ce5e12f09@domain.hid"
 type="cite">
  <pre wrap="">Actually, the test you proposed:

=============
            # Unselect unresolved residues.
            if not UNRES:
                unselect.read(name, file=UNRES)
=============

should not include not.  The statement needed is that if the UNRES
file exists, use it to deselect the residues.  It currently say that
if the UNRES file does not exist, use it to deselect the residues.
Sorry, I should have seen that one.

Regards,

Edward


On Jan 10, 2008 10:17 PM, Sebastien Morin <a class="moz-txt-link-rfc2396E" \
href="mailto:sebastien.morin.1@domain.hid">&lt;sebastien.morin.1@domain.hid&gt;</a> \
wrote:  </pre>
  <blockquote type="cite">
    <pre wrap=""> I tried the line a you proposed :

 UNRES = None

 and it yields an error.

 relax&gt; unselect.read(run='tm0', file=None, dir=None, change_all=0,
column=0)
 RelaxError: The file name argument None must be a string.

 However,

 UNRES = 'None'

 does not yield this error and the script proceeds...

 Am I right ?


 S&eacute;b  :)







 Edward d'Auvergne wrote:
 On Jan 10, 2008 9:59 PM, Sebastien Morin <a class="moz-txt-link-rfc2396E" \
href="mailto:sebastien.morin.1@domain.hid">&lt;sebastien.morin.1@domain.hid&gt;</a> \
wrote:


 Thanks Ed !

 Another similar would maybe ease life of users without PDB or with small
proteins... We could add the possibility of not having any file for
unresolved residues...

 The lines :
 =============
 # The file containing the list of unresolved residues to exclude from the
analysis.
 UNRES = 'unresolved'
 =============

 could become :
 =============
 # The file containing the list of unresolved residues to exclude from the
analysis (set this to None if no residue is to be excluded).
 UNRES = 'None'
 =============

 This should be:

UNRES = None

rather than a string. The user will instantly see the problem if
'None' is supplied as a string. But this is a good idea, so feel free
to make the changes. Don't forget to port the changes to the 1.3 line
using 'svn merge'.

Regards,

Edward




--
Sebastien Morin
Etudiant au PhD en biochimie
Laboratoire de resonance magnetique nucleaire
Dr Stephane Gagne
CREFSIP (Universite Laval, Quebec, CANADA)
1-418-656-2131 #4530


    </pre>
  </blockquote>
  <pre wrap=""><!---->
  </pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">-- 
Sebastien Morin
Etudiant au PhD en biochimie
Laboratoire de resonance magnetique nucleaire
Dr Stephane Gagne
CREFSIP (Universite Laval, Quebec, CANADA)
1-418-656-2131 #4530
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