This is just to tell you that I am actually measuring amide protons (NH). Sorry for the mistake but I was reading/writing the email in a hurry. I still didn't have the time to work further on this but meanwhile I was thinking and remembered that Tensor2 allows saving the PDB file in the diffusion frame. If I use this rotated pdb file and choose Zero degrees for all Euler angles I should be able to overcome the problem with the reference definition, no?
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Edward d'Auvergne Sent: terça-feira, 1 de Dezembro de 2009 14:10 To: tpais Cc: [email protected] Subject: Re: MF_Multimodel Hi, >> 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 Note that there is a problem with missing theory here. First you need the CSA value. Then you need the dipole interaction vector, which in this case is 2 actually vectors. In Abragam's relaxation equations used in all model-free programs there is a key assumption which fails - that the CSA tensor and the dipolar interactions are collinear. Even if the CSA component of relaxation is negligible, the 2 NH vectors point in different directions which will intersect the diffusion tensor at different positions and hence have different relaxation rates (the spectral density functions are direction dependent, so different directions have different J(w) values). But you also have movement of the sidechains causing this to be somehow averaged out (I'm unaware of any theory for treating this yet). In addition, you have crazy interference (cross-correlated relaxation) between NH1, NH2, and H1H2. You will really have to see what others have done before you to handle this mess, and then try to determine if any model-free program out there will handle such a nightmare situation (relax, Modelfree4, Dasha, and Tensor2 do not). >> 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? This is an argument to the structure.read_pdb() user function. This now defaults to the internal reader. >> 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. Maybe if you created a bug report and attached to it some truncated files (data and script) which reproduce the problem (the data subset can be randomised if you are worried about it being online). If I can run and test it myself, then I should be able to spot the problem instantly and have a fix in hopefully ~5 min. Cheers, Edward _______________________________________________ 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
