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 _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
