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phenix.superpose_pdbs_1.4
by David Garboczi 07 Feb '09

07 Feb '09

The default unit cell and symmetry for the "fitted" model (the one that was moved) is the unit cell and symmetry of the "fixed" pdb. As I am superimposing the same model from several space groups to study the differences in packing, I need the "fitted" pdb to keep its own unit cell and symmetry. How might I do this? When is the current default of altering the unit cell and symmetry of the moving model useful? thanks, Dave --

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TLS in phenix.refine_gui
by Miles Pufall 03 Feb '09

03 Feb '09

Hi Guys - Is there a way to load the TLS groups, generated so kindly by TLSMD in old phenix format, into the new gui? It would save a lot of typing. Thanks! Miles Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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modification of nonbonded geo restraints between symmetry mates
by Alejandro Buschiazzo 03 Feb '09

03 Feb '09

Dear PHENIX users, I wonder what is the 'correct' way of (re)defining geometric restraints among atoms. Here's what I need to do : I have several cations that are chelated by protein residues; some of them involve residues from the same monomer, yet others involve atoms from both the ASU monomer as well as crystal neighbors (i.e. symmetry mates). I see that in the .geo file, these parameters are taken into account as nonbonded simple and nonbonded asu respectively ... how can I change the ideal distances to get proper Zn+2 coordination bonds for both kind of partners? Thank you in advance for your help! -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185

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map coeffs?
by Walter Novak 03 Feb '09

03 Feb '09

Hi all, I am doing joint X-ray neutron refinement, and in the 1.4-3 version I now get twice the number of choices of map coefficients when opening the mtz. Half now have "no_fill" with them. I am assuming that the difference between maps has something to do with missing Fobs, is that right? Which maps should I be looking at then? Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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TLS + anisotropic ADP mixed refinement
by Scott Classen 03 Feb '09

03 Feb '09

I am trying to perform refinement on a model with three chains (two protein and one DNA... plus water, Cl, and a few other solventy things). The B factors for chain A are generally better than for the other two and I am thinking that the resolution (1.8Å) warrants attempting anisotropic individual adp refinement for at least chain A, and then using TLS for the other two. So my strategy is: *individual_sites *individual_adp *tls *occupancies adp.individual.isotropic = "not Chain A" adp.individual.anisotropic = "Chain A" adp.tls = "Chain B" adp.tls = "Chain D" Previously the model had only been refined with individual isotropic adp (no TLS). The starting model has an r_work=0.2079 and r_free=0.2427. With this new aniso/TLS strategy in the first macrocycle when it gets to the initial TLS refinement it completely blows up with r_work and r_free both going up to 60% have I specified my refinement with bad syntax? or is this even possible with phenix.refine? I can submit more of the log file if you're interested. Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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can phenix.refine calculate r_work and r_free without doing refinement?
by Scott Classen 02 Feb '09

02 Feb '09

Hi all, I was wondering if phenix can calculate r_work and r_free without refinement, sort of like the model_stats from CNS. Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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phenix version 1.4-3: problem with bulk solvent scaling
by Oliv Eidam 31 Jan '09

31 Jan '09

Hi, I am currently refining a good 1.6 Angstroem data set using Phenix. Thereby I noticed a significant difference of R-free (>3%) depending on whether I used phenix version 1.3-rc6 (installed on my Mac laptop) or phenix version 1.4-3 (installed on my linux work station). Rfree differs by more than 3% (!) although I am using the same starting model, the same reflection file and the same refinement protocol (shown at the end of this email with detailed R and R-free factors for the 3 steps). In my opinion, my phenix 1.4-3 installation has a problem in the "bulk solvent modeling and scaling" steps. Indeed, I find in the log file that the "overall anisotropic scale matrix" shows all values set to zero. Analogous the "maximum likelihood estimate for coordinate error". This is true in all steps where an "overall anisotropic scale matrix" is calculated. Here is one example during 1.4-3 refinement: ====================== bulk solvent modeling and scaling ====================== |--(resolution: 1.61 - 29.59 A; n_refl. = 99535)------------------------------| | | | r_work= 0.3419 r_free= 0.3358 ksol= 0.39 Bsol= 19.12 scale= 1.247 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: -0.00 A | | x-ray target function (ml) for work reflections: 5.981207 | |-----------------------------------------------------------------------------| The same example during 1.3-rc6 refinement: ===================== bulk solvent correction and scaling ===================== |-macro cycle = 1-(resolution: 1.61 - 29.59 A; n_refl. = 99537)---------------| | | | r_work= 0.3153 r_free= 0.3064 ksol= 0.40 Bsol= 43.79 scale= 1.087 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-4.01,-5.36,-8.20,-0.00,2.74,0.00); trace/3= -5.86 | | | | maximum likelihood estimate for coordinate error: 0.33 A | | x-ray target function (ml) for work reflections: 5.946583 | |-----------------------------------------------------------------------------| I am asking now: Did something go wrong during my Phenix installation? I already re-installed Phenix (no errors): same result. Do I have to change something in my input files? I should probably mention that "bulk_solvent_and_scale = True" in my input .def files. Any help appreciated. Many thanks, Oliv -------------------------------------------------------------------------------- Refinement protocol and development of R and Rfree during each refinement round: -------------------------------------------------------------------------------- 1)Rigid body refinement 2) Simulated annealing (5000K) 3) Ordered solvent (plus annealing @ 2000K) phenix version 1.3-rc6: 1) R=31.5, Rf=30.6 2) R=23.9, Rf=25.8 3) R=19.8, Rf=22.0 phenix version 1.4-3: 1) R=31.6, Rf=30.6 2) R=27.8, Rf=29.8 3) R=23.7, Rf=25.2 -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email: eidamo(a)blur.compbio.ucsf.edu

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joint xn refinement question
by Walter Novak 30 Jan '09

30 Jan '09

Hi, I am new to the list, but I didn't see this issue in the list archive. I am doing a joint refinement using x-ray and neutron data (each set is ~2.0 Å). I added H positions using reduce and have been switching to Ds as the density suggests for exchangeable positions. My problem is that I cannot seem to get the H (or D) positions to refine into the neutron density. Perhaps I need an additional command, so I am attaching my refinement script. I can provide a few pictures from coot to demonstrate if helpful. Thanks! Wally phenix.refine prot_joint4_r8_001.pdb \ neutron_data.file_name=prot_best_mcH_D2O_2_data.mtz \ xray_data.file_name=prot_best_mcH_D2O_2_data.mtz \ output.prefix=prot_joint4_r9 \ strategy=rigid_body+individual_sites+individual_adp \ simulated_annealing=False \ input.xray_data.labels=F-obs input.neutron_data.labels=F-obs-neutron \ input.xray_data.r_free_flags.label=R-free-flags \ input.xray_data.r_free_flags.file_name=prot_best_mcH_D2O_2_data.mtz \ input.xray_data.r_free_flags.test_flag_value=1 \ input.neutron_data.r_free_flags.label=R-free-flags-neutron \ input.neutron_data.r_free_flags.file_name=prot_best_mcH_D2O_2_data.mtz \ input.neutron_data.r_free_flags.test_flag_value=1 \ main.number_of_macro_cycles=5 \ restraints_edits.params \ refinement.hydrogens.refine=individual \ find_and_add_hydrogens=True \ switch_to_isotropic_high_res_limit=2.5 \ optimize_wxc=true \ optimize_wxu=true \ --overwrite Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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Site-wide defaults for phenix.refine parameters
by Stephen Graham 29 Jan '09

29 Jan '09

Hi all, Apologies if I've missed this in the documentation, but is there any way to set 'site-wide' defaults for, say, phenix.refine? That is, I'd like to modify the default parameters for phenix.refine so that occupancy refinement is turned off by default, the output.serial_format is different, geo files aren't created, always use F/SIGF not I/SIGI, etc. Cheers, Stephen P.S. I know I can change this by hand in my .def file and then propagate the .def file through subsequent rounds of refinement for a given project. It would just be nice to have my default personal preference parameters set (~/.phenix?) so I don't need to change them each time I start a new project... -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

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occupancy refinement
by Nicole Bischoff 29 Jan '09

29 Jan '09

Dear all, in my electron density I can see negative difference density (fo-fc) for the carboxyl groups of some aspartates or glutamates. Assuming that this is a result of partial decarboxylation due to radiation damage, I wanted to refine the occupancies of these carboxyl groups. To this end, I set the occupancy of these atoms to 0.99 in Coot so that they would be picked up by occupancy refinement in phenix.refine (using version 1.4-3). Phenix however just put the value back to one. It looks like the occupancy refinement in phenix is meant for alternative conformations where the sum of the occupancies of the different conformations is 1. How can I make phenix refine partially decarboxylated acidic side chains? It does not seem appropriate to me to make alternative conformations, one with and one without the carboxyl group. That would look funny at my resolution (2.7 Angstrom) and might not fix the problem. Any hints are appreciated. Thank you, Nicole ---- Nicole Bischoff, M. Sc. PhD student in the Gruetter lab Department of Biochemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland +41 44 635 5556 nbischoff(a)bioc.unizh.ch

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