Hi Dave, Sorry for the delayed response, I have just returned from holidays. Please see below:
On 4 June 2015 at 17:02, Lawrence David Finger <d.fin...@sheffield.ac.uk> wrote: > I posed these questions some time ago, but I have not heard from anyone or > whether my message was accepted by the moderator. I guess I am not on the > list. Below is what I wrote initially. I just checked the mailing list backend, and your d.finger email address is not present. You should try subscribing again. One step that is often forgotten is that after you receive the subscription request email and follow the link, you have to in that page specifically select to subscript or ignore the subscription. In most cases when you are not subscribed, the mailing list maintainer Chris MacRaild will see your message and accept it. One problem though is that public mailing lists are a massive magnet for spam. So if your message is buried in a pile of 1000 spam messages, it is sometimes not seen and thrown out with the 1000 junk messages. Being subscribed to the list avoids this. > We have a question concerning our results from our latest calculations using > relaxGUI. We have fed the program NMR relaxation data at 500 and 600 MHz on > the free protein and a structure of the protein in complex with DNA from an > X-ray structure. We know that binding of DNA induces some secondary > structures because the free protein has sections missing in the pdb. Because > the free protein structure has residues missing presumably due to disorder in > the crystal, we chose to use the structure of the bound protein. Could the > use of a structure of our protein with more order than expected cause > problems with the selection of the rotational diffusion tensor? Very much so! If there is a conformational change, you should probably split the protein in 2 and analyse each domain or rigid body separately. > The diffusion tensor the program has selected doesn’t seem to match the > overall shape of the protein. If it can cause a problem, how do I add the > residues missing from the crystal structure for the refinement? Furthermore, > can the program handle some residues missing in crystal structures? The problem with a non-spherical model-free analysis is that the average XH bond vector orientation in solution is a core requirement of the theory. If this is incorrect, this can lead to either of the two well known artefacts: - Artificial nanosecond motions (the Schurr 1994 paper). - Artificial Rex value (the Tjandra 1995 paper). See my 2007 Mol. Biosyst. paper at http://dx.doi.org/10.1039/b702202f for a review about this problem and how this relates to the under or overestimation of the vector projection within the diffusion tensor. One way to handle this situation is to use what I have termed a 'hybrid' model. For residues which have no structural information, you can use the local tm model and avoid a global correlation time, and linearly combine these models with the global diffusion tensor models applied to all known residues. You could even shift residues with high beta factors from the global Brownian diffusion model into the 'local tm' model category. relax will allow you to do this, but it will require a bit of manual work. So if you know you have two domains with large structural rearrangements, you can perform three analyses: - Local tm for missing residues. - The full protocol for domain 1. - The full protocol for domain 2. Then combine the final results as one model. There should be zero overlap of residues in these 3 divisions. You could then compare this, using AIC values to take parsimony and non-nested model differences into account, to a local tm model for all residues. Note that the local tm models are generally quite noisy if data from < 3 fields are used. I hope this helps. Regards, Edward _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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
