Hi, I'm new to Relax and I'm having some trouble running a model free analysis with my data. In short, all the spins are being deselected, supposedly because of missing structural data even though I have loaded a PDB of the structure.
Some details of the system: I'm using Relax 4.0.0 with scripts under Win7 Pro 64 The molecule is a homodimer and I have R1, R2, hetNOE data at 600 and 700 MHz The data is only from 5 spins out of 31 (for a chain, both chains being identical) The pdb is from a crystal structure (so, no proton) What I've done so far: I've run the dauvergne_protocol.py with 'local_tm' and 'sphere' without problem. 'sphere' converged after 5 rounds. Both gave 'aic' solutions (but then, I think they are not using the PDB directly). However, when I run any of 'prolate', 'oblate', 'ellipsoid', the script end up with "no model selected...'aic' pipe not created". Looking at the console output, it seems that after the data is loaded fine and dAuvergne_protocol() starts: - pipe is created OK - local_tm is read OK - model_free.remove_tm() is run OK - diffusion_tensor.init() is run OK - fix() is run OK Then: - minimise.grid_search() starts and deselects all the spins: "Over-fit spin deselection... because of missing structural data" Of course, after this, the grid search does not work. I'm thinking that my system is far from standard for this type of analysis, and there are a few possibilities for things going wrong, starting with the fact it's a homodimer, and that the spins with data are in limited numbers (although they are spatially well distributed). But I have no ideas how/where/why, so I'm a bit stuck for now. Does anyone have an idea? I've attached a screenshot and the first 3 scripts in case that helps. If you need anything else, please ask. I've also noticed something that's probably not related, but just in case: it seems that the function minimise.grid_search() starts with 'inc=11' even if I passed 'GRID_INC=13' in my script (through dAuvergne_protocol() )...If it's not expected, and other variables are somehow not updated, this might be the cause of the problems. Best, Alain The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE. _______________________________________________ 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
