Hi Anna, to find out what's going on I just did the following: 1) I copied the lines below into "answer.pdb" file and I re-set the occupancies so they all make sense (add up to 1); 2) Using "answer.pdb" file I simulated two datasets: X-ray and neutron: "data.mtz". What I did is just I computed X-ray and neutron Fcalc, and called their absolute values as F-obs-xray and F-obs-neutron, and stored them in "data.mtz". 3) Then I scrambled the model in "answer.pdb" by randomizing the occupancies of all atoms. This file containing the scrambled models is called "start.pdb". 4) Finally, I took "data.mtz" and "start.pdb" files and ran joint XN refinement in phenix.refine. I did only occupancy refinement. As the refinement result I was expecting to get the PDB file with refined structure where all the occupancies are exactly the same as in "answer.pdb". The command I used is: phenix.refine data.mtz start.pdb params --overwrite 5) Now, open two files "answer.pdb" and "refinement_result_001.pdb", and voila! All the occupancies are as expected. All the input and output files discussed above are located here: http://cci.lbl.gov/~afonine/for_AnneG/ All the above data and files manipulations were done using "phenix.pdbtools" and "phenix.refine". Could you reproduce the refinement I just did ("step 4") using your version of PHENIX ? If not, then please update to the latest PHENIX (http://www.phenix-online.org/download/) and try again. If not successful even then, I will send you the latest development version. Please let me know if you have any questions or problems! Pavel. On 2/10/2009 11:04 AM, Anna Gardberg wrote:
I am doing joint refinement of a perdeuterated protein, and I am having a problem with alternate conformations - the deuterium occupancies don't match the overall occupancies for their conformation:
ATOM 335 N APRO A 19 13.154 0.897 15.243 0.38 8.64 N ATOM 336 CA APRO A 19 12.556 0.209 16.391 0.38 7.61 C ATOM 337 CB APRO A 19 13.743 0.043 17.350 0.38 12.47 C ATOM 338 CG APRO A 19 14.713 1.102 16.926 0.38 9.70 C ATOM 339 CD APRO A 19 14.594 1.126 15.443 0.38 13.59 C ATOM 340 C APRO A 19 11.414 0.974 17.057 0.38 13.42 C ATOM 341 O APRO A 19 10.559 0.334 17.671 0.38 15.65 O ATOM 342 DA APRO A 19 12.236 -0.672 16.112 0.48 5.78 D ATOM 343 DB2APRO A 19 13.454 0.173 18.268 0.43 15.49 D ATOM 344 DB3APRO A 19 14.128 -0.841 17.229 0.52 10.36 D ATOM 345 DG2APRO A 19 14.460 1.959 17.300 0.60 13.82 D ATOM 346 DG3APRO A 19 15.610 0.852 17.197 0.30 14.04 D ATOM 347 DD2APRO A 19 14.850 1.996 15.097 0.48 12.84 D ATOM 348 DD3APRO A 19 15.119 0.413 15.046 0.40 8.63 D ATOM 349 N BPRO A 19 13.163 0.886 15.240 0.62 8.58 N ATOM 350 CA BPRO A 19 12.606 0.252 16.438 0.62 7.70 C ATOM 351 CB BPRO A 19 13.777 0.307 17.423 0.62 11.89 C ATOM 352 CG BPRO A 19 14.973 0.224 16.548 0.62 11.13 C ATOM 353 CD BPRO A 19 14.616 1.094 15.375 0.62 13.76 C ATOM 354 C BPRO A 19 11.399 0.972 17.012 0.62 13.34 C ATOM 355 O BPRO A 19 10.491 0.304 17.514 0.62 15.31 O ATOM 356 DA BPRO A 19 12.371 -0.680 16.253 0.23 7.26 D ATOM 357 DB2BPRO A 19 13.760 1.148 17.905 0.72 12.42 D ATOM 358 DB3BPRO A 19 13.734 -0.446 18.034 0.19 14.30 D ATOM 359 DG2BPRO A 19 15.759 0.552 17.012 0.87 14.63 D ATOM 360 DG3BPRO A 19 15.094 -0.695 16.264 0.40 9.68 D ATOM 361 DD2BPRO A 19 14.807 2.022 15.580 0.43 11.93 D ATOM 362 DD3BPRO A 19 15.083 0.798 14.578 0.31 8.63 D
I am using these refinement options: refine { strategy = *individual_sites *rigid_body *individual_adp group_adp tls \ *occupancies group_anomalous sites { individual = None rigid_body = None } occupancies { individual = None remove_selection = None constrained_group { selection = None } } }
and hydrogens { refine = *individual riding refine_adp = one_b_per_residue one_b_per_molecule *individual refine_occupancies = one_q_per_residue *one_q_per_molecule individual contribute_to_f_calc = True } What refinement options should I be using to keep the D occupancies the same as the rest of their conformation? Hope you can help!
Regards, Anna