i get it -- May 21, 2012 - 13:11

so i have to make a script specific for my data. i just formatted my data files like the ones in the sphere and simply transferred them to relax in the programs files and this i think is where the problem may lie, my data is simply not being read correctly isn't it? so i bet i have to go back to the drawing board.

regards

Jimmy

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From: Edward d'Auvergne <edward@xxxxxxxxxxxxx>
To: James Nyirenda <jamesn7414@xxxxxxxxx>
Cc: "relax-users@xxxxxxx" <relax-users@xxxxxxx>
Sent: Monday, 21 May 2012, 18:55
Subject: Re: format of the pdb

Hi Jimmy,

Are you using the dauvergne_protocol.py script or the same analysis
built into the GUI (the auto-analysis)?  I would recommend using this
auto-analysis for model-free when you have multiple field strength
data.  For the message, I would guess that the problem is that there
is a mismatch with the PDB file.  To solve or understand such
problems, it would be useful to have more information.  For example
the relax user function you ran which gave these warnings, and maybe
one of the 'N' atom lines from the PDB file itself.  Actually, the
full output from relax would be much more useful (you can use '$ relax
--log my_log my_script.py' to obtain a full log in the 'my_log' file).
Possibly copying and pasting the contents of the script (not
attaching) would also be useful.

The warning you see says that it cannot find atom number 1, named 'N'
for residue 433 in the PDB file.  You can check this manually.  The
number 1, the atom number, is the first column of the PDB.  The
residue number and atom name should hopefully be obvious.  I'm
guessing that earlier in the script you have loaded into relax,
sequence data which does not match what is in your PDB file.
Alternatively, your 'N' atoms are called something else in the PDB.  I
hope this helps,

Regards,

Edward



On 21 May 2012 11:44, James Nyirenda <jamesn7414@xxxxxxxxx> wrote:
> Dear all, i tried to test both the windows based and mac based relax
> programs and used the sphere for modelfree analysis, it worked alright but
> would like to test my small data set, i have already r1,r2 and noe at two
> fields but would like to know how to input the pdb so that vectors can be
> extracted.
> i get a message like this
>
> "RelaxWarning: Cannot find the atom in the structure (atom ID ':433@1&@N').
> RelaxWarning: Cannot find the atom in the structure (atom ID ':434@12&@N')."
> etc----
>
> Jimmy.