Hi,
If you are using the script based UI (user interface) then, yes, you
will have to modify the scripts to suite your data. You will have to
start again from scratch, and the auto-analysis of the
dauvergne_protocol.py script could take up to 1-2 weeks (if you have a
slow computer). Have you used this script previously? If not, how
did you perform your analysis? Did you write new scripts to implement
one of the old analyses from 2 decades ago?
As for the data not being read in correctly, I cannot possibly answer
yes to this while is still know nothing ;) The amount of information
provided is nowhere near enough to be able to know what has been done,
what data has actually gone into relax, or what is happening. So
maybe the problem is something else. It's equivalent to me saying my
car won't start, and then asking if the spark plug gap is correct for
my engine type. Or asking if I need to replace my computer RAM
because my computer won't turn on. It would be useful to have more
information to be able to know what the problem really is.
Regards,
Edward
On 21 May 2012 13:11, James Nyirenda <jamesn7414@xxxxxxxxx> wrote:
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
________________________________
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.
Re: i get it