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R-free problem with phenix.refine
by Vinson LIANG 22 Oct '10

22 Oct '10

Dear all, Recently I deposited a structure to PDB. However, I was told >> The R value of SF check are different from your reported value. >> >> R work in SF check = 0.2859 >> your reported R work = 0.1474 >> Also there are no R free flags in your sending files, but you reported R >> free value in your all deposition. So, I rerun my deposited file with phenix.refine, and it gave a R-work=0.1475, R-free=0.1742. However, when I tried to run the same file with refmac5, error came with "Free R label has not been set". I guess phenix.refine gives Rree-R label that other program could not recognize. Could anyone please help me to solve this problem? Thank you very much in advance. I don't know why structure refined with phenix.refine has such problem. I wish this problem will disappear in the future, since I so like phenix.refine. Best, Vinson,Liang

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refine : peculiar TLS tensors
by Bryan Lepore 22 Oct '10

22 Oct '10

[ phenix 1.6.4-486 ] [ ALSO : tlsanl, refmac, etc. from ccp4 6.1.3 ] [ molscript/povscript ] the one-liner : i have some TLS tensors that sometimes do not compare at all well with refmac/anisoanl tensors. sometimes, the principal axes of a TLS tensor refines *very* far away from the center of mass(=center of reaction), or the axes from tlsanl are exceptionally small as if not scaled properly. the eigenvalues are really small too. see [*] for troubleshooting and strategy used. i suspect i am missing something. i also understand this might not be a phenix question. -bryan [*] i compared another .def that gave sensible TLS results with a different dataset/model, and my {} are all good AFAIK. anisoanl/refmac/parvati results are reasonable. the phenix refinement appears well behaved. these are all using tlsextract to get the eigenvalues/origins, and molscript to check the axes/centers of mass. input B factors are Beq unless i made an error. the tls group selections can vary - however, simple groups also can give these results. in general, using strategy (excerpt) : refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp *tls *occupancies *group_anomalous sites { individual = None torsion_angles = None rigid_body = None } adp { individual { isotropic = None anisotropic = None } group_adp_refinement_mode = *one_adp_group_per_residue \ two_adp_groups_per_residue group_selection group = None tls = "chain A and (resid 1:41 or resid 42:159 or resid 195:237 or resid 263:420)" tls = "chain A and resid 160:194" tls = "chain A and resid 245:252" } [...cut off ... ] example output of an ill-behaved S tensor from tlsanl : SCREW ROTATION AXIS ABSOLUTE POSITION (A) PITCH (A) X Y Z 1 70.667 154.197 308.627 -144.435 2 977.334 819.588******** 6222.947 3 640.7191431.084 471.341 269.382

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maps : sigma-a
by Lepore, Bryan 21 Oct '10

21 Oct '10

how might one start to go about getting phenix to automatically write out the value of sigma_A vs. resolution? e.g. when making maps, to get that nice table in Randy Read's SIGMAA program output of ln(sigma_A) vs. resolution. -bryan

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Bad ligand parameters
by Joe Krahn 21 Oct '10

21 Oct '10

I found that residue TRS has different dihedral target angles for the three hydroxyl oxygens, which are actually all equivalent. They have a periodicity of 1, but should have a periodicity of 3. What is the best way to handle such discrepancies? Most ligand parameters are probably auto-generated based on a reference structure, and there is probably a lot of conformation bias. In this case, it seems that parameterization should have been able to detect symmetry. It would be nice if parameters could include information about whether a human has done any validation. Actually, a ligand Wiki might be nice, where people can easily put comments, even if they are not sure about how to improve the parameters. Joe Krahn

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refine : a priori TLS tensor eigenvalues
by Bryan Lepore 21 Oct '10

21 Oct '10

[ phenix 1.6.4-486 ] i gather that phenix.refine will not take a priori refined TLS tensor eigenvalues - either from input or from the pdb header. is this right? -bryan

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Joint X-ray/Neutron Refinement
by Louis Lazar 21 Oct '10

21 Oct '10

Hello, Sorry for reposting, I am trying to get a better response with a more detailed subject line. I am seeing an internal error while trying to conduct joint x-ray/neutron refinement, and any help with the issue below would be greatly appreciated. Thank you very much in advance: ================================ ADP refinement=============================== Traceback (most recent call last): File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/driver.py", line 1182, in run call_back_handler = call_back_handler) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py", line 735, in refinement_machine h_params = h_params) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py", line 192, in __init__ all_params = all_params) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py", line 216, in refine_adp model.set_refine_individual_adp() File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/model.py", line 1035, in set_refine_individual_adp iselection = selection_iso.iselection()) RuntimeError: cctbx InternalError: /net/anaconda/scratch1/phenix/phenix-1.6.4-486/cctbx_project/cctbx/xray/scatterer_flags.h(417): CCTBX_ASSERT(f.use_u_iso()) failure. This error occurs during the 2nd macro cycle of refinement using this general command: phenix.refine model.pdb data_xray.hkl neutron_data.file_name=data_neutron.hkl input.xray_data.labels=FOBSx input.neutron_data.labels=FOBSn Thanks again. Regards, Louis

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Stretched Maps
by Joel Weadge 21 Oct '10

21 Oct '10

Hi all,I have just finished doing molecular replacement and an initial round of refinement (with simulated annealing) on a number of different datasets. They have all be straightforward since most of them are either point mutants and/or co-crystal structures. However, two of the structures are giving me some trouble. The data appears to be of good quality and resolution (2.25 and 2.55Å). The MR proceeds as normal with good scores and then in the subsequent round of refinement the maps (2Fo-Fc and Fo-Fc) look strange. The density is stretched or flattened in one direction. Can anyone help me with what I may be overlooking?Thanks in advanceJW

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occupancy refinement of a metal ion
by Christian Roth 20 Oct '10

20 Oct '10

Dear all, if I understood the manual correctly I could refine the occupancy and set the B-Factor to a constant value, or vice versa. Is there a possibility that phenix refine the B-Factor automatically to the value of the coordinating residues and adjust than the occupancy to a good value? I seems to be that the metal site is not fully occupied. I guess I have to set the B-value manually to the value of the surrounding residues and do than a refinement, right? Best regards Christian

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fix rotamers question
by Peter Grey 20 Oct '10

20 Oct '10

Dear Phenix community, I would like to have some additional information regarding fix_rotamers. In particular : - How Phenix chooses which rotamers need to be fixed ? - Does Phenix really re-calculate the three maps after correcting each rotamer ? For very large structures this is very time-consuming and one can settle for calculating a new map every 10-20 residues. Perhaps this could be a user-controlled parameter ? -Can you please explain how fix_rotamers works together with ncs restraints ? Thank you in advance for shedding light on this, Peter

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about low resolution refinement
by crystallogrphy 18 Oct '10

18 Oct '10

Hi, I am refining a low resolution data. According to sigma vs. resolution, my resolution is 4.7A. Because there are four identical molecular per asymetric unit, I can use positional refinement. There are about 65% alpha-helices in the structure, so I want to use secondary structure restrain. Does phenix has this restrain in the refinement? I am using Phenix-1.4 version.

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