Hi, thanks for your quick reply, even during weekend!
Another problem is that
there are so many different ways of specifying the tensor, and most
programs that can calculate a tensor don't give you enough information
for fully defining the thing. E.g. Blackledge's Tensor program and
Art Palmer's Modelfree program use different definitions for the
spherical angles for the spheroids and Euler angles for the ellipsoids
(good luck finding these).
Yes, I was afraid this would be a problem! I was feeling lucky....
Therefore with the iterative procedure,
you can watch the tensor rotate to the correct position.
Ok,will follow the iterative procedure
Note that you can specify what the isotope is using the value.set()
user function. The exact element is, from memory, only used when
calculating the centre of mass, so I don't think this is very
important for what you are calculating. It really depends what you
are doing here. HH appears only to be the hydroxyl proton in Tyr and
the terminal NH2 protons in Arg. HZ is attached to CZ in Phe, the
terminal NH3 protons in Lys, and protons attached to carbons in Trp.
Are you measuring NH2 and NH3 relaxation? If so, which theories would
you like to use to interpret the data?
I am measuring NH2 relaxation and will be using Lipari-Szabo Modelfree
The internal reader accepts
these CONECT records perfectly. An easy test is to read in the PDB
file with CONECT records with the internal reader and then write it
out again. They should be preserved. If not, this is a bug which can
be reported at https://gna.org/bugs/?func=additem&group=relax which I
can then repair.
I think the mf_multimodel script uses the internal reader...what is the
command to read with the internal reader?
Can you make a bug report for this? This should be allowed - and if
not it is a bug.
Sure
This could be related to point 3 above. Did you see any optimisation
when running the script? Were there any RelaxWarning messages anyway
through the analysis?
Couldn't notice any warning message but it actually didn't seem to be doing
anything because all the values were the same.
There are a series of *.display() user functions that can be used to
see individual values. E.g. value.display() and
diffusion_tensor.display(). The XML version is for data storage, and
not designed for being a compact representation of the data. It is
human readable though, just not the most efficient way to see the data
using human eyes. You can also use value.write() if you would like
the individual data dumped into a file.
Thanks!
I think your help has been very usefull. I'll find out in the netx days
when I am back to the lab.
Best Regards,
Tiago P
Re: MF_Multimodel