Re: PDB orientationRe: PDB orientation|
Hi Ed, Your comments are interesting... but nevertheless trouble me... I talked with the guy who makes the MD simulation with my protein. He noticed that some NH vectors indeed have motions well defined by a cone which is fine if we want to analyze things with the model-free approach. However, some NH vectors have motions more like a stretched cone (which is not surprising at all, since motions inside a protein are restricted by the available space as long as with the position of charges, etc), More worrying are some motions seen as two separate cones, which is then bad, since an average position doesn't have any meaning and can even be impossible due to steric or charge problems... Ok. The reason I would not use a crystallographic structure is that maybe some NH vectors could be badly oriented because of packing modifications in the crystal (at interfaces)... An NMR structure may be better, but impossible for a lot of people, like me... But what does the individual NH vector orientation really affect ? Will a different NH vector orientation give rise to a different selected model or will it only affect model parameters ? Also, will some bad NH vector orientations (let's say less than 10% bad orientations overall) affect the global diffusion parameters ? In other words, will those possibly bad orientations produce artifacts, like false Rex or modified tm, for example ? Another question... The NH vectors are described by two coordinates (for H and N) in the PDB files, but transformed to angles within relax or any program alike (Am I right ?). Can a user directly input a set of angles rather than coordinates ? I ask this because I'd like to try to input average orientation which were computed to give a set of angles rather than a modified PDB file... Are the coordinates necessary to analyze the global diffusion (to assess the shape of the protein) ? Are the angles only used for local motions analysis ? Thanks for the tips / opinions / comments / anything ! Cheers Séb :) Edward d'Auvergne wrote: Hi, I have to say that I am definitely not an expert in this subject. When I have this issue I just use Molmol to add the protons, which I would assume is based on ideal geometry. For any simulation I would guess that the proton will move around in and out of the peptide plane. So, if you can assume that this motion is accurately simulated which, if done correctly, these fast motions should be then maybe the average position would be the best for model-free analysis. Be careful though because this is a whole can of worms you could be opening here! Model-free analysis (as well as many other theories in the field) assumes in its theory that you have a defined bond vector orientation but the analysis implies motion which in turn means the vector moves again in turn changing the results of the analysis. Note the circular loop of dependence and the lack of theory addressing this - this really is not an issue for the faint hearted! Regards, Edward On 10/24/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:Hi Ed Thanks for the information about the relative PDB orientation and Euler angles... For adding hydrogens to a PDB, I wonder what approach is best so that it can be used (in relax) for non isotropic relaxation analysis. In other words, what approach would be best to get good NH vector orientations ? I have a PDB at 1.95 A resolution and without any hydrogen. I tried two different approaches to get the hydrogens in a good orientation... 1. Hydrogens were added inside CHARMM and then a short Langevin minimization (200 ps) was done. 2. Hydrogens were added inside CHARMM (as for approach 1) and then a molecular dynamics simulation was performed (by another PhD student) with TIP3P water and 3 snapshots were taken at time 10, 12 and 14 ns (after 2 ns equilibration)... I could take snapshots up to 40 ns, but they should be equivalent to others... My questions : What approach do you think is the best to get good NH orientations ? Would it be relevant to take different snapshots from MD and use them in separate relax runs ? Would you suggest another approach ? Cheers Sébastien :) Edward d'Auvergne wrote: Hi, The only differences in the analysis should be due to different bond orientations. The PDB reference frame doesn't matter - this will only change the values Euler angles of the diffusion tensor and nothing else. So if the same structure exists in two different PDB frames, then the difference in the optimised Euler angles will be solely due to the rotation between the two structures. If you were to change the PDB frame in any of your files, the final chi-squared value should be identical to a non-rotated PDB. The differences you do see are because the relative XH bond orientations in the different structures are different. Regards, Edward On 8/30/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote: Hi, I am doing different tests with the full_analysis.py script, data at three magnetic fields and different PDB structures (taken from MD simulations). I realized that those different structures give rise to different optimization times and also to different chi-squared values for the different diffusion tensors (I have only tried the prolate diffusion tensor). I wonder if the structures need to be processed before giving as inputs for relax. Especially, do the structures need to be centered relative to their inertia tensor (like with the pdbinertia program that one should use prior to model-free analysis using ModelFree). Thanks ! Sébastien :) -- ______________________________________ _______________________________________________ | | || Sebastien Morin || ||| Etudiant au PhD en biochimie ||| |||| Laboratoire de resonance magnetique nucleaire |||| ||||| Dr Stephane Gagne ||||| |||| CREFSIP (Universite Laval, Quebec, CANADA) |||| ||| 1-418-656-2131 #4530 ||| || || |_______________________________________________| ______________________________________ _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list relax-users@xxxxxxx 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 -- ______________________________________ _______________________________________________ | | || Sebastien Morin || ||| Etudiant au PhD en biochimie ||| |||| Laboratoire de resonance magnetique nucleaire |||| ||||| Dr Stephane Gagne ||||| |||| CREFSIP (Universite Laval, Quebec, CANADA) |||| ||| 1-418-656-2131 #4530 ||| || || |_______________________________________________| ______________________________________ -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne CREFSIP (Universite Laval, Quebec, CANADA) 1-418-656-2131 #4530 |