- phenixbb - phenix-online.org

refinement with alternative molecules?
by Su-Chang Lin 27 Jan '10

27 Jan '10

Hi, Recently I got a crystal structure of a multiple-molecules protein complex. There are many protein subunits with the same fold. From the likelihood-weighted maps by Phenix, I can see two different subunits occupy the same position. (So I can put the model of either subunit in the same densities, but some loop regions and the C-terminal tail look different. ). I know Phenix can do occupancy refinement with a residue that has N alternative conformations. My question is can Phenix do occupancy refinement with alternative molecules? The RMSD for two subunits is about 1.3 angstrom. The sequence identity is about 30%. Thank you very much! Su-Chang Lin, Ph.D., Postdoc Associate Department of Biochemistry Weill Medical College, Cornell University Whitney Building, room W-212 1300 York Avenue, New York, NY 10021 212-746-6458

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phenix.fmodel: a command line tool to compute structure factors from a model (Fcalc or Fmodel).
by Pavel Afonine 27 Jan '10

27 Jan '10

Starting PHENIX nightly build version 1.6-295 (2010-01-27), a new command line tool phenix.fmodel is available. This is a replacement for "phenix.pdbtools --f-model" command, which is not available anymore. phenix.fmodel is a comprehensive tool to compute structure factors from a model. For more information and usage examples simply run phenix.fmodel . Pavel. P.S. Below is the result of running phenix.fmodel: phenix.fmodel: a tool to compute structure factors, Fmodel: Fmodel = scale * exp(AnisoScale) * (Fcalc + k_sol * exp(-b_sol*s^2/4) * Fmask) where: - Fmodel - total model structure factor (complex value) - AnisoScale = -ht*A(-1)*b_cart*A(-1)th/4 - h - column vector with Miller indices - A - orthogonalization matrix - b_cart - anisotropic scale matrix - t and (-1) denotes transposition and inversion operations - scale - overall scale factor - Fcalc - structure factors calculated from atomic model - k_sol and b_sol - Flat Bulk solvent model parameters - Fmask - structure factors calculated from bulk solvent mask Usage examples: 1) phenix.fmodel model.pdb high_resolution=1.5 will result in a file containing complete set of Fmodel = Fcalc computed from atomic model up to 1.5A resolution. 2) phenix.fmodel model.pdb scale=2 k_sol=0.35 b_sol=50 b_cart="1 2 3 0 4 7" high_res=1.5 low_res=10 will result in a file containing complete set of Fmodel computed using the above formula in resolution range 1.5-20.0A. 3) phenix.fmodel model.pdb high_resolution=1.5 algorithm=direct is similar to "1)" but the Fcalc are computed using direct summation algorithm. 4) phenix.fmodel model.pdb high_res=1.5 format=cns label=FOBS type=real r_free=0.1 will result in CNS formatted file containing complete set of amplitudes of Fmodel = Fcalc computed up to 1.5A resolution, labelled as FOBS, and free-R flags with 10% of test reflections. This is a typical command to simulate Fobs. 5) phenix.fmodel model.pdb high_res=1.5 scattering_table=neutron will result in a file containing complete set of Fmodel = Fcalc computed from atomic model up to 1.5A resolution using neutron scattering table. 6) phenix.fmodel model.pdb parameters.txt will result in a structure factor file, where Fmodel were computed using parameters defined in parameters.txt file. The parameters.txt file can contain all or any subset of parameters listed below. Note, that each { must have a matching one }. 7) phenix.fmodel model.pdb reflection_data.mtz will result in a file containing a set of Fmodel = Fcalc that will match the set of Miller indices of the data in reflection_data.mtz file. 8) phenix.fmodel model.pdb reflection_data.mtz data_column_label="FOBS,SIGMA" similar to "7)", where the specific data array is selected. See below for complete list of available parameters. ------------------------------------------------------------------------------- Parameters to compute Fmodel:: high_resolution = None low_resolution = None r_free_flags_fraction = None add_sigmas = False scattering_table = wk1995 it1992 *n_gaussian neutron data_column_label = None fmodel { k_sol = 0.0 b_sol = 0.0 b_cart = 0 0 0 0 0 0 scale = 1.0 } structure_factors_accuracy { algorithm = *fft direct cos_sin_table = False grid_resolution_factor = 1/3. quality_factor = None u_base = None b_base = None wing_cutoff = None exp_table_one_over_step_size = None } mask { use_asu_masks = True solvent_radius = 1.11 shrink_truncation_radius = 0.9 grid_step_factor = 4.0 verbose = 1 mean_shift_for_mask_update = 0.1 ignore_zero_occupancy_atoms = True ignore_hydrogens = True } output { format = *mtz cns label = FMODEL type = real *complex file_name = None } anomalous_scatterers { group { selection = None f_prime = 0 f_double_prime = 0 } }

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occupancy refinement
by Christian Roth 27 Jan '10

27 Jan '10

Dear all, I refine a structure of a protein to 1.4 A and found a few SO4-Ions. I tried to refine this sulfurs and some of these seems to be not fully occupied, as the negative difference density suggest. I tried to refine the occupancy of the sulfate ions to get an idea how strong the different binding sites might be occupied. All sulfate ions are in Chain C of my pdb. I tried to refine the occupancy individually using refine.occupancy.individual SO4 but this lead to different occupnacies for every atom for every atom and theix cant be the case for sure. Then I tried and group occupancy with resname=SO4 but now every sulfate ion has the same occupancy, which is indicated from my previous refinements also not the case, because two ions have no negative difference density. At the momentI can not figure out how I should combine the keywords for the individual occupancy refinement of the different sulfate ions. In my structure. Should I define for every ion a different chain or how I could overcome this problem? I would be very happy if anyone has a idea to sove this problem or tell me what keyword I misunderstood in the documentation. Best regards Christian

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GUI for Auto-MR
by Laurie Betts 27 Jan '10

27 Jan '10

I installed version PHENIX 1-5-2 under Linux, and the main GUI has an option for AutoMR Phaser that says (old PHENIX GUI) - if that crashes is it because we don't have the old GUI installed? THe other main items seem to work fine. The last error message in the terminal window seems to suggest that is the case.... Thx, Laurie BEtts

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twin data set
by r n 26 Jan '10

26 Jan '10

Hi I did processed a data set, which seems P3. I did molecular replacement and end up with solution with higher R factor. Then, I did used xtriage to check the data, it gave me possible space group P321 and few twin laws, this space group did not given me any solution , data seems have translation symmetry along z axis? Also I did processed in P1 and did molecular replacement end up in high R-factor. I really appreciate if any one has any suggestion what is going on with data? I given log file from xtriage, --------------------------------------------------------------------------------------------- | Point group | mean R_used | max R_used | mean R_unused | min R_unused | BIC | choice | ---------------------------------------------------------------------------------------------- | P 3 | None | None | 0.314 | 0.027 | 8.149e+03 | | | P 6 2 2 | 0.314 | 0.460 | None | None | 1.856e+05 | | | P 3 2 1 | 0.027 | 0.027 | 0.446 | 0.432 | 5.667e+03 | <--- | | P 6 | 0.432 | 0.432 | 0.249 | 0.027 | 1.856e+05 | | | P 3 1 2 | 0.460 | 0.460 | 0.242 | 0.027 | 1.859e+05 | | ---------------------------------------------------------------------------------------------- Statistics depending on twin laws ------------------------------------------------------------------ | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------ | -h,-k,l | M | 0.432 | -0.009 | 0.046 | 0.022 | | h,-h-k,-l | M | 0.027 | 0.450 | 0.478 | 0.478 | | -k,-h,-l | M | 0.460 | -0.012 | 0.049 | 0.022 | ------------------------------------------------------------------ Patterson analyses - Largest peak height : 34.261 (corresponding p value : 7.017e-04)

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map averaging
by Gabriela Guédez 25 Jan '10

25 Jan '10

Hi dear Phenixbb, Is there a command tool to make ncs density averaging in a high oligomerization model that has some maps clearer than others? not multi-crystal but the same crystal. Thank you, Gabriela -- ---------------------------------------------------------------------- Gabriela Guédez R. gabriela.guedez(a)bzh.uni-heidelberg.de

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how to convert .cif with multiple datasets
by Zheng Zhou 24 Jan '10

24 Jan '10

Dear phenix experts: I am using phenix.cif_as_mtz to convert a .cif file downloaded from pdb, but when I run ################################################ phenix.cif_as_mtz XXXX-sf.cif Sorry: Crystal symmetry is not defined. Please use the --symmetry option. ################################################ Then I run ############################################### phenix.cif_as_mtz XXXX-sf.cif --symmetry=XXXX.pdb Multiple data sets found => ignored: XXXX-sf.cif What should I do? Thanks for your help. Joe

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explicit pdb output file name (refine)
by Ed Pozharski 21 Jan '10

21 Jan '10

Do I understand correctly that there is no way to force refine to skip the serial in the output pdb file name, i.e. foo.pdb, not foo_001.pdb? -- Ed Pozharski <epozh001(a)umaryland.edu> University of Maryland - Baltimore

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polygon resolution control
by Young-Jin Cho 21 Jan '10

21 Jan '10

Hi I was using polygon from GUI. One question I have now is how I can control the resolution limit. As I cut the resolution during refinements but polygon gave me from the uncut-high resolution. Is there any way, I can ask polygon to get statistics upto certain resolution as shown on pdb file? As always, thanks in advance. YoungJin

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Re: [phenixbb] polygon resolution control
by Alexandre Urzhumtsev 21 Jan '10

21 Jan '10

Dear YoungJin >I was using polygon from GUI. One question I have now is how I can control >the resolution limit. As I cut the resolution during refinements but >polygon gave me from the uncut-high resolution. Is there any way, I can >ask polygon to get statistics upto certain resolution as shown on pdb file? Honestly, I do not know for the phenix version; let's wait what Pavel & Nat answer you. Very probably they already implemented it and your problem will be solved easy. Another simple solution will be to cut explicitly your MTZ file by the resolution you wish before run the polygon. If not, such an option (to define explicitely the resolution; that will select for comparison the PDB structures refined previously at such a resoluton) exists in the original Tcl/tk based version of the polygon. Please, let me know if your are interested in it. Best regards, Sacha

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occupancy refinement default selections - bug or feature?
by Ed Pozharski 21 Jan '10

21 Jan '10

There is a ligand residue in the structure that have its occupancy set to 0.75. refine with default parameters apparently refines every atom individually, so in the end I have a strange situation where ligand atoms have different occupancies. Of course, regular alternate conformers in the protein part of the structure have single occupancy refined per residue. Interestingly, when I place altLoc identifier "A" in front of the residue name of the ligand, single occupancy value is refined (although there is no second conformation). It settles down near 0.7 (close to what I selected previously based on a traditional approach of eliminating difference density and roughly matching B-factors of hydrogen-bonded protein atoms with ligand), so apparently constraints (e.g. total occupancy for all the conformers) are not applied. Is this intentional behavior (I understand that groups can be defined in the input file but adding altLoc letter seems like a simple trick)? I think most people would initially expect that occupancy will not vary within a residue, so the default behavior may seem like a bug to some (the only situation I can think of where such variation is justified is to model radiation damage). -- Ed Pozharski <epozh001(a)umaryland.edu> University of Maryland - Baltimore

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Dear everybody
by YuYong Tao 21 Jan '10

21 Jan '10

Dear everybody: I installed phenix-1.6, when i run 'phenix.solve', it showed as follows: ustc-lifescience:~> phenix.solve binary=/usr/local/phenix-1.6-288/build/intel-linux-2.6/solve_resolve/exe/solve SOLVEDIR=/usr/local/phenix-1.6-288/solve_resolve/ext_ref_files SYMOP=/usr/local/phenix-1.6-288/solve_resolve/ext_ref_files/symop.lib SYMINFO=/usr/local/phenix-1.6-288/solve_resolve/ext_ref_files/syminfo.lib CCP4_OPEN=UNKNOWN SOLVE_RESOLVE_MALLOC_MAX=399459600 /usr/local/phenix-1.6-288/build/intel-linux-2.6/solve_resolve/exe/solve: error while loading shared libraries: libsvml.so: cannot open shared object file: No such file or directory and when i run 'phenix.resolve' ,it seems to be ok. So i donn't know what to do. Can you tell me? Best Wishes!

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How do different sections of TLS groups affect refinment
by Bart, Aaron G 21 Jan '10

21 Jan '10

Greetings everyone, I am still fairly new to crystallography, so forgive me for my naivety. My question involves how the TLSMD server segments my protein and the effects it has on refinement. For instance when i use "Multi-Chain Alignment Analysis", which lines the sequence for all of my chains (a total of 12) and shows how TLS groups are divided among them, it shows varying selections of TLS groups among the different chains. It should be noted that the sequence is the same for all the chains in my protein. Also if a TLS group splits a alpha helix into multiple parts, would this be valid? I have come to understand that helices move more like rigid bodies than segmented groups... Thanks! -Aaron

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K(sol) and B(sol)
by J. Fleming 20 Jan '10

20 Jan '10

Hi, I'm working on a structure but am having problems with K(sol) and B(sol). What are they and how do I get them into range? I thought they might have something to do with my waters but I have no water B-factors <25. Thanks for any help! -Jon

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twin refinement in phenix-1.5-2
by Kelly Daughtry 19 Jan '10

19 Jan '10

Hello all, I am wondering if anyone has run across this problem and knows how to fix it. I have a twinned dateset and I am using phenix.refine to refine the dataset. I have the full 1.5-2 installation. When I include the twin law (-k, -h, -l) in the refinement, I get this error: File "/usr/swr/phenix-1.5-2/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1651, in map_coefficients "m_gradient" AssertionError If I do not include the twin law, I do not get the error and the refinment continues as normal. When I downgraded to Phenix.1.4-3 (full install), And use the same twin law, I am able to run phenix.refine without an error. I have attached my definition file for phenix.1.5-2 amd the log file. Thanks in advance for any help you can provide, Kelly Daughtry ******************************************************* Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 *******************************************************

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Reflection file conversion
by Nate Nicely 19 Jan '10

19 Jan '10

I use d*TREK to reduce my data and phenix.reflection_file_converter to import the data. I seem to have had a bit of trouble generating the free R flags. It seems that the cap for the max number of free R reflections takes precedence over the percentage, even when the percentage is given expressly on the command line. I find myself setting the cap artificially high on the command line so that a full 10% is set aside. I was taught to set aside 10% for the free R set, only going lower if setting aside the full 10% compromised completeness. I'm just wondering what is the rationale for the numeric cap? Am I making any error(s) with my methodology? Nate N

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Re: [phenixbb] clash guarde failure phenix coot
by Pavel Afonine 19 Jan '10

19 Jan '10

Hi Georg, I think the refinement .log file should contain the lines like these below: Warning: very small nonbonded interaction distances. Nonbonded interactions: 12604 Sorted by model distance: nonbonded pdb=" CG ARG A 3 " pdb=" CG ARG A 4 " model vdw 0.000 3.840 nonbonded pdb=" NE ARG A 3 " pdb=" NE ARG A 4 " model vdw 0.000 3.200 which pinpoints you the offending atoms. Does this answer your question? Pavel. On 1/19/10 9:57 AM, Georg Mlynek wrote: > > Dear All, > > I´m refining a 2.1A with phenix 1.5-2 and get when I click on > automatically add hydrogens to model following error message: > refinement.pdb_interpretation.clash_guard.failure: Number of nonbonded > interaction distances < 0.5:391 > > I suppose that this comes, because coot mixes up the hydrogens. >

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rigid body refinement problem
by Jianghai Zhu 19 Jan '10

19 Jan '10

Hi, I am using phenix.refine_dev_282 for a rigid body refinement. The output pdb file is exactly the same as the input model even though there are obviously some large movements. Here are some information from the log file. Information about total rigid body shift of selected groups: rotation (deg) translation (A) xyz total xyz total group 1: 0.051 -5.493 -1.073 5.60 0.55 -3.15 -1.35 3.47 group 2: 0.254 0.562 0.252 0.67 0.36 -3.99 0.87 4.10 group 3: 3.807 4.001 -2.262 5.92 -0.81 -3.17 1.06 3.44 group 4: 2.275 -4.215 1.909 5.12 -0.18 -2.95 -1.43 3.28 group 5: -1.902 -5.750 -3.206 6.81 -1.99 -4.44 0.27 4.88 group 6: -4.932 -3.939 -5.340 8.16 -0.18 -2.08 -0.25 2.11 group 7: -1.140 -0.769 -7.715 7.83 0.73 -2.91 0.04 3.00 group 8: 2.008 -1.858 -1.236 3.02 -1.10 -5.44 -0.82 5.61 But then the model didn't change at all. stage Deviation of refined model from start model max min mean 0 : 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 1_rbr: 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 1_adp: 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 Is this a bug? -- Jianghai

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difference density map
by 丁玮 19 Jan '10

19 Jan '10

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Where is phenix.refine finding starting r values?
by Bart, Aaron G 19 Jan '10

19 Jan '10

Greetings, I am fairly new to crystallography, and have just started to use Phenix for structural refinement. I am currently working on a 2.8A structure that was run through multiple rounds of rigid body refinement via Refmac and manual revision using Coot. I eventually got stuck where large portions of my molecule had very poor density and the rwork and rfree stayed around 0.3. I then performed a TLS refinement which resulted in better density, and tried running it through phenix.refine with default ADP settings, as well as simulated annealing. It worked beautifully, however when I looked at the log file for the refinement, phenix was reporting a starting rwork and rfree that represented my first stage of refinement in refmac, 0.38/0.44. My question is, is phenix somehow neglecting the refinement that was done in refmac? Regards -Aaron

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Re: [phenixbb] merohedral twinned refinement
by JXQI 19 Jan '10

19 Jan '10

Zwart, Cherney and all, Thanks for the suggestions.The problem is fixed when I tried P31. Best regards J.X. Qi > > 3. If I try P3,the Matthews coeffs tell 2 or 3 molecules in the ASU,the > molecules will crash.Besides,the overall FOM ( lower than 0.4) and the > R/Rfree values (about 0.45/0.56) suggest that the P3 is the wrong sg. try P31 or otherwise P1. You should get a solution in those groups. It could of course mean that there are OD type issues, but I would not jump there yet. Can you send the intensity statistics from xtriage?

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right symmetry?
by Gabriela Guédez 18 Jan '10

18 Jan '10

Hi Phenixbb, I have a data that indexes in P6122, also P61 and P31. Data analysis in phenix.xtriage says no twinning is suspected according to the L-test. However, after MR and twin RB refinement, the model improves from P6122 or P61 to P31 5% Rfacs and 0.5 the FOM. I thought the data might have RPS and twinning not detected with the L-test. So, i ran xtriage to compute the RvsR statistics using the obs_and_calc.mtz file and the results were: in P61 R_abs_twin observed data : 0.112 R_abs_twin calculated data : 0.047 in P31 R_abs_twin observed data : 0.117 R_abs_twin calculated data : 0.139 "misespecified crystal symmetry", according to Lebedev, Vagin, Murshudov et al 2006, Acta Cryst. D62,83-95. I would like to know a test that tells me the right symmetry. I appreciate your help. Thanks, Gabriela

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Re: [phenixbb] merohedral twinned refinement
by JXQI 18 Jan '10

18 Jan '10

Dr.Zwart, Thanks for the reply. 2. The systematic absences and the Rsym support the P3121.I already mentioned the model fit very with the map if I use the P3121. 3. If I try P3,the Matthews coeffs tell 2 or 3 molecules in the ASU,the molecules will crash.Besides,the overall FOM ( lower than 0.4) and the R/Rfree values (about 0.45/0.56) suggest that the P3 is the wrong sg. 4. TLS refinement also did not imrove the results. 5. There are totally 88 aa in my protein, I could build 86 aa clearly. The intensity ststistics is attached in the message. J.X. QI ************************************************************************ Shell I/Sigma in resolution shells: Lower Upper % of of reflections with I / Sigma less than limit limit 0 1 2 3 5 10 20 >20 total 50.00 4.95 0.9 1.5 1.9 2.4 2.8 4.0 9.5 90.5 100.0 4.95 3.93 0.0 0.2 0.3 0.5 0.8 2.0 6.6 93.4 100.0 3.93 3.44 0.2 0.3 0.6 1.0 2.5 5.4 15.4 84.6 100.0 3.44 3.12 0.0 0.2 0.5 0.7 2.5 7.6 22.7 77.3 100.0 3.12 2.90 0.3 1.0 2.1 3.2 7.2 17.6 41.4 58.6 100.0 2.90 2.73 0.0 0.7 2.0 3.2 9.9 20.8 52.9 47.1 100.0 2.73 2.59 0.0 1.4 2.9 5.7 12.4 30.0 60.8 39.2 100.0 2.59 2.48 0.7 1.6 4.7 7.7 16.3 36.0 71.5 28.5 100.0 2.48 2.38 0.6 2.1 5.0 10.2 21.9 42.0 76.2 23.8 100.0 2.38 2.30 0.8 2.3 7.4 12.7 25.3 49.4 83.4 16.6 100.0 All hkl 0.4 1.1 2.7 4.7 10.0 21.1 43.4 56.6 100.0 Summary of reflections intensities and R-factors by shells R linear = SUM ( ABS(I - <I>)) / SUM (I) R square = SUM ( (I - <I>) ** 2) / SUM (I ** 2) Chi**2 = SUM ( (I - <I>) ** 2) / (Error ** 2 * N / (N-1) ) ) In all sums single measurements are excluded Shell Lower Upper Average Average Norm. Linear Square limit Angstrom I error stat. Chi**2 R-fac R-fac 50.00 4.95 619.8 13.8 3.5 1.039 0.046 0.050 4.95 3.93 834.6 17.5 5.0 1.156 0.048 0.052 3.93 3.44 521.9 14.6 4.5 1.026 0.059 0.062 3.44 3.12 333.7 11.1 4.1 1.073 0.071 0.068 3.12 2.90 172.5 7.1 3.6 1.153 0.098 0.096 2.90 2.73 131.4 6.0 3.4 1.256 0.116 0.108 2.73 2.59 102.8 5.2 3.4 1.306 0.140 0.130 2.59 2.48 77.7 4.6 3.4 1.381 0.173 0.158 2.48 2.38 64.1 4.3 3.3 1.355 0.195 0.177 2.38 2.30 54.7 4.1 3.3 1.345 0.221 0.197 All reflections 297.8 8.9 3.7 1.209 0.071 0.059 Intensities of systematic absences h k l Intensity Sigma I/Sigma 0 0 2 -0.2 0.4 -0.5 0 0 4 0.1 1.0 0.1 0 0 5 0.4 1.4 0.3 0 0 7 1.1 2.5 0.4 0 0 8 0.4 2.1 0.2 0 0 10 7.3 3.4 2.2 0 0 11 6.0 3.5 1.7 0 0 13 -2.3 4.9 -0.5 0 0 14 6.1 4.3 1.4 0 0 16 8.1 5.1 1.6 0 0 17 3.9 4.9 0.8 0 0 19 0.8 4.5 0.2 0 0 20 4.0 4.6 0.9 ********************************************************************* 1. How do the intensity statistic look like? 2. How did you choose P3121? 3. Did you try solving and refining in P3? 4. TLS? 5. How complete is your model 2010/1/17 JXQI <jxqi at mail.im.ac.cn>: > Dear all, > > I have a 2.3A data set processed with HKL2000. The space group is P3121 with > 63% of solvent content and 1 molecule in the ASU. I used a 40% homology > model to do molecular replacement. Both the Phaser and Molrep gave similar > solution with good packing. After further refinement with phenix, the built > model fit well with the 2mFo-DFc map. However the R/Rfree were stuck to > 0.34/0.38. > > I rechedked the data set with xtriage and found the data set is merohedral > twinned (with twin law"-h,-k,l", the estimated twin fraction is about 0.05). > When I used the twin law in further refinement, the R/Rfree were only > decreased to 0.32/0.36. Any suggestions are appreciated, thanks! > > > J.X. QI > _______________________________________________ > phenixbb mailing list > phenixbb at phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

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merohedral twinned refinement
by JXQI 18 Jan '10

18 Jan '10

Dear all, I have a 2.3A data set processed with HKL2000. The space group is P3121 with 63% of solvent content and 1 molecule in the ASU. I used a 40% homology model to do molecular replacement. Both the Phaser and Molrep gave similar solution with good packing. After further refinement with phenix, the built model fit well with the 2mFo-DFc map. However the R/Rfree were stuck to 0.34/0.38. I rechedked the data set with xtriage and found the data set is merohedral twinned (with twin law"-h,-k,l", the estimated twin fraction is about 0.05). When I used the twin law in further refinement, the R/Rfree were only decreased to 0.32/0.36. Any suggestions are appreciated, thanks! J.X. QI

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Twin fraction in phenix refine
by Pietro Roversi 18 Jan '10

18 Jan '10

Dear all, phenix.xtriage estimates a twin fraction of between 24 and 30% but then when I start the refinement I get 47-49%. In CNS if I fix the twin fraction in a series of refinements the Rfactors jump from 44% (twin fraction 0) to 37% (from 25% to 49%, only marginal improvement upon going from alpha=25% to 49%). Questions: 1. Is the refinement of alpha dependent on the model? 2. I am tempted to work with the 30% that xtriage estimates but do not know how: is there a way to fix alpha? Thanks Pietro -- Sent from my Desktop Pietro Roversi EP Abraham Fellow in Biochemistry - Lincoln College - Oxford Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385

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Re: [phenixbb] [ccp4bb] Adding H in refinement
by Schubert, Carsten [PRDUS] 13 Jan '10

13 Jan '10

Hi Pavel, sorry I hijacked the thread a bit... A question about the riding Hydrogens and their B-factors. I noticed that at least with earlier versions of PHENIX the B-factor of the Hydrogens was not fixed to the B-factor of the bonded atoms. If I would generate the Hydrogens in reduce they would inherit the appropriate B-factors, but during the course of the refinement and rebuilding they would start to diverge, sometimes drastically. Are you saying the current implementation restrains the B-factors to the bonded atoms and forces them to be equal or are they just inherited and are allowed to float afterwards? Cheers, Carsten > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Pavel Afonine > Sent: Tuesday, January 12, 2010 12:24 PM > To: CCP4BB(a)JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Adding H in refinement > > Hi Sara, > > - what you observe should not happen since phenix.refine uses riding > model for H atoms. The hydrogen's B-factors are automatically inherited > from the atoms these hydrogens are bonded to. For example, in X-H bond > the B-factor of X should be equal to B-factor of H. > > - make sure you are using the latest version of PHENIX: > http://www.phenix-online.org/download/ > > - if this does not help, please contact me directly, and send the data > and model so I can tell you what exactly is not right (all the files > will be handled confidentially). > > - there is PHENIX bulletin board: > http://www.phenix-online.org/mailman/listinfo/phenixbb > > Pavel. > > > I did refinement with phenix of my 1.9-2.0 Angstroem structures and > included the hydrogens (riding). However, when I checked on the > statistics (refinement close to the end), the average B-factor was > extremely high (in phenix.polygon it was higher than with any other > structure in similar resolution range). It makes sense though that this > happens, if you have a residue which has a high B-factor and carries a > lot of hydrogens the average B-factor will raise quite a lot (since the > B-factor of hydrogens is calculated 1-1.5x of B-factor from the atom > it sits on), right? > > (When I removed the hydrogens again, the average B-factor was > fine...) > > > > My question is now did I do something wrong in my refinement (-> do I > have to change something that this does not happen), or is this > something everybody sees? > > > > If this is common, what would happen (during evaluation) if you want > to publish a structure and the statistics show such a high average B- > factor? Is it better to have hydrogens on, but a bad average B, or no > hydrogens on and a good average B... Obviously, I never published a > structure ;) > >

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Beamtime at the ALS
by Peter Zwart 12 Jan '10

12 Jan '10

Dear All, January 15, 2010 is the deadline for the March/April 2010 Rapid Access Proposal cycle. All Berkeley Center for Structural Biology(BCSB) beamlines are equipped with ADSC Q315/Q315R detectors, automated sample changers and data collection software enabling high-throughput crystal screening and data collection. Remote data collection is available on all BCSB beamlines, providing the user with the full complement of sample visualization, sample manipulation, beamline control, data acquisition and data analysis tools exactly as they would see them if they were stationed at the beamline. This enhanced remote operation capability is coupled with 22hr onsite support by BCSB staff who are able to assist immediately with loading additional samples for remote users or troubleshoot any issues that might arise. Remote users can furthermore be kept up-to-date on changes in ring status via an SMS service (http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Ph…) Specific features are summarized below. Beamlines 8.2.1 and 8.2.2: To facilitate studies on small crystals, a microdiffractometer was installed in the beamline 8.2.1 endstation. The new equipment allows precise sample positioning to within 2 microns, excellent sample viewing of very small crystals, and an off-axis crystal positioning stage. Both beamlines 8.2.1 and 8.2.2 feature a Rigaku sample changer (Actor), allowing remote operations to now be a routine mode of access for these beamlines. Beamlines 5.0.1, 5.0.2, 5.0.3: The Berkeley Automounter sample handling system has a routine capacity of 96 samples (6 pucks). In a typical high-throughput screening mode, the mount-to-mount time is around 2.5 minutes per sample, allowing users to screen a full puck within 45 minutes. The sector 5 beamline user stations are equipped with fully high-adjustable, ergonomically friendly work stations. Data analyses in the BCSB is facilitated by software maintained by sbgrid (http://www.sbgrid.org). A 16 core linux machine is available for our users to process their data and solve/refine their structure. An additional mode of access to the BCSB beamlines is through the Collaborative Crystallography (CC) Program. Users apply for beamtime via the general user program, and collaborate with an expert crystallographer who will conduct the experiments and data reduction on behalf of the researchers. Depending on the users, structure solution, model building and refinement can be carried out as well. Please contact BCSBBeamtime(a)lbl.gov for more information. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/ Scroll down to "Structural Biology beamines (includes protein SAXS)." Click on "New Proposal." If you'd like to apply for May/June 2010 beamtime at the Advanced Light Source, please submit a General User proposal by March 15, 2010. If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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January 15, 2009 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 12 Jan '10

12 Jan '10

Dear Users, The deadline for Mar/April 2010 Collaborative Crystallography proposals will be *January 15, 2009. * ------------------------------------------------------------------------ Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ----------------------------------------------------------------------------------------- How To Apply: To learn more, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for Mar/April 2010 allocation period, proposals must be submitted by *January 15, 2009.* The deadline for CC proposals for the time period May/June 2010 will be March 15, 2010. Regards, Banumathi Sankaran

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reduce and ready_set problem
by Jianghai Zhu 11 Jan '10

11 Jan '10

Hi, I believe I have reported this bug before, but it is not fixed in the phenix.reduce and phenix.ready_set yet. The problem is the hydrogens added by reduce when there is a glycan. Here is the error message. Number of atoms with unknown nonbonded energy type symbols: 12 "ATOM 8332 HD22 ASN B 99 .*. H " "ATOM 11820 HD22 ASN B 320 .*. H " "ATOM 12615 HD22 ASN B 371 .*. H " "ATOM 14058 HO4 NAG B3320 .*. H " "ATOM 14086 HO4 NAG B3321 .*. H " "ATOM 14136 HO4 NAG B3371 .*. H " "ATOM 22458 HD22 ASN D 99 .*. H " "ATOM 25955 HD22 ASN D 320 .*. H " "ATOM 26750 HD22 ASN D 371 .*. H " "ATOM 28256 HO4 NAG D3320 .*. H " ... (remaining 2 not shown) ... Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 12 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). The hydrogen left on the N atom of the ASN is correct, but should be named as HD21 as defined in the ccp4 cif library. And the HO4 for the NAG glycan is just wrong. I have to delete all these hydrogens to get phenix.refine going. -- Jianghai

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Resolve after Phaser SAD module - question
by Peter Grey 10 Jan '10

10 Jan '10

Dear Phenix experts, It is recommended to use FWT/PHWT after Phaser SAD module for initial map calculation. Could you please explain how to tell Resolve to pick these fields for the initial map ? With MR it is clear since you need FWT and PHIC but with SAD you really need FWT and PHWT . I thank you in advance, Peter

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Phenix.refine RuntimeError
by JXQI 10 Jan '10

10 Jan '10

Dear PHENIXBBs, I tried to refine a N-linked glycan using phenix.refine and used the data_link=NAG-ASN for ASN-NAG connection. But I got a RuntimeError of unknown atom_id: HD22. From the mon_lib_list.cif file of Phenix-1.5-2, the atom_id HD22 is already defined. Any suggestions are appreciated. Thanks J.X. QI ********************************************************* Monomer Library directory: "/home/jxqi/152Phenix/phenix-1.5-2/chem_data/mon_lib" Total number of atoms: 11844 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain A and resname ASN and resid 170 residue_selection_2: chain A and resname NAG and resid 1 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain C and resname ASN and resid 170 residue_selection_2: chain C and resname NAG and resid 1 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain E and resname ASN and resid 170 residue_selection_2: chain E and resname NAG and resid 1 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Traceback (most recent call last): File "/home/jxqi/152Phenix/phenix-1.5-2/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/jxqi/152Phenix/phenix-1.5-2/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/home/jxqi/152Phenix/phenix-1.5-2/phenix/phenix/refinement/command_line.py", line 227, in __init__ self.pdb_file_names) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/utils.py", line 907, in process_pdb_files stop_if_duplicate_labels = stop_if_duplicate_labels) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/utils.py", line 940, in _process_pdb_file log = self.log) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2995, in __init__ log=log) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2105, in __init__ log=log) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1575, in __init__ prev_mm=prev_mm) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 543, in __init__ mod_mod_id=self.mon_lib_srv.mod_mod_id_dict[apply_data_mod]) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 819, in apply_mod mod_mon = self.monomer.apply_mod(mod_mod_id) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/cif_types.py", line 359, in apply_mod result.delete_atom_in_place(mod_atom.atom_id) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/cif_types.py", line 264, in delete_atom_in_place raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id) RuntimeError: delete_atom_in_place: unknown atom_id: HD22 **********************************************************

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Hello
by Pankaj Chauhan 06 Jan '10

06 Jan '10

Hello, While during NCS based restrained refinement, how can we take two chains as single translation unit as the pdb model is a dimer-dimer. Thanks -- Pankaj Chauhan Senior Research Fellow, PhD Scholar Crystallography Laboratory Division of Protein Science & Engg. IMTECH , Chandigarh, INDIA

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coot - display map
by r n 06 Jan '10

06 Jan '10

Hi I am using Phenix GUI, after refinement , tried to load the coot interface in Phenix, it opens up the coot, but did not load the map or model file. I am using coot0.6 version, Is there any place in phenix enviroment that I could mention the path for coot? Thanks

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refinement
by r n 05 Jan '10

05 Jan '10

Hi I am doing refinement using phenix. I did simulated annealing, Rfree goes up to 10% more than before. (40%) and R stays at 35%. If use previous phenix refinment file for same pdb and data , R and Rfree is 25/27%. I thought even different r-free set after simulated annealing and 7 cycles of refinement in phenix should bring Rfree down, but not ? But same data set and model , in CNS, R/Rfree 26/28%. Any suggestions will be appreciated. I am using phenix-dev249 - linux. thanks ram

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text output for model quality and validation report at phenix
by Ravindra D. Makde 04 Jan '10

04 Jan '10

Hi all, I will greatly appreciate the answers to following query: How can I get the text or excel output of the model quality and validation report of a model after phenix refinement? I am specially interested in real space CC of the various residues. I am using phenix.refine_gui at phenix-1.4-162. I have searched all output files, but couldn't find. Thanks in advance. Ravi Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA

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optimize phenix
by r n 04 Jan '10

04 Jan '10

hi all I am trying to optimize the model, in which secondary structures are distorted and I did pdbtools , geometry regulatization , after optimization still the helices are distorted. Is it any tools in the phenix that could optimize the secondary structures alone in the pdb? Thanks ram

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some sort of occupancy refinement
by Bryan W. Lepore 01 Jan '10

01 Jan '10

question is after the setup here : i have a ligand with multiple conformers. i gave each conformer a different chain label. refining occupancy for the overlapped parts kicks that part out of the density. i have remove_selection for the parts that are 1.0 and they seem OK. a single conformer stays in the density. i tried starting with and without site or occupancy refinement, no help. i do not want group occupancy refinement b/c some parts do not overlap - i.e. they "should" be occupancy 1.0 -- i tried it anyways with constrained_group =... to check. is the chain label an improper way to do this? -bryan p.s: Happy New Year with Blue Moon Eclipse (~10degW->180degE long. eastern HS)!

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high resolution Anomalous map
by vennila Natesan 31 Dec '09

31 Dec '09

Hello all... How do we create anomalous map using high resolution reflections? For example, if we have 2.2A resolution data (i.e 20-2.2A), i want to know how to create the anomalous map for the same dataset but from 2.4-2.2A resolution range. Vennila.

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phenix.refine change: support for residues on symmetry elements
by Ralf W. Grosse-Kunstleve 28 Dec '09

28 Dec '09

The current development version of phenix.refine (dev-268 or later) supports residues located on symmetry elements, e.g. SO4 on a three-fold axis. phenix.refine now computes structure factors slightly differently compared to older versions. The new rules are: - Atoms with occupancy == 1 are subject to automatic handling of the symmetry. Example: An atom near a three-fold axis (distance to symmetry copy <= 0.5 A) is moved onto the axis and constrained in refinement to stay on the axis. The "special position factor" (1/3 is this case) is taken into account internally. The factor does not appear in the occupancy. - Atoms with occupancy != 1 are assumed to take the special position factor into account in the occupancy. Automatic handling of the symmetry is turned off. Example: A disordered SO4 molecule near a three-fold axis should have occupancies of 0.33 for all atoms. - If all atoms in a residue have occupancies != 1, all nonbonded symmetry interactions between the atoms in the residue are disabled. These three rules are meant - to bring phenix.refine in line with other programs and the PDB. - "to do the right thing" in most cases without manual intervention. Please let me know if you see problems with the new way phenix.refine uses occupancies to determine special position constraints and exclusions for nonbonded symmetry interactions. Does anyone need atoms with partial occupancies but constrained to stay on a symmetry axis during refinement? Ralf

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Re: [phenixbb] Phaser SAD question
by Kitty Pattridge 24 Dec '09

24 Dec '09

"Randy J. Read" <rjr27(a)cam.ac.uk> wrote: >Dear Peter, > >I'm interested in your observation that you get better signal from an >anomalous difference map computed with density-modified phases than you get >with an LLG map using the MR model. Presumably the density modification >just started from the model phases as well? We've never tried that, so >we'll have to look into that. Unfortunately, you can't at the moment start >the LLG completion with a "model" specified through structure factors, >though this is on our to-do list. > >With the MR+SAD option, because it is iterative, there are sites found in >subsequent cycles (where the information from some of the anomalous >scatterers has become available) and you end up with a set of reliable >sites that can be significantly larger than the set obtained from the first >LLG map. Does your anomalous difference Fourier with density modified >phases give you a larger apparently reliable substructure than the >iterative completion? You could use phenix.emma to compare the two >substructures and see how much they have in common. > >You can indeed give Phaser the set of sites that you got from the anomalous >difference map. One way to choose the cutoff would be to see how deep the >deepest hole is (i.e. how many standard deviations the map goes in the >negative direction), and choose a larger number in the positive direction. >Or you could just use the peaks above 6-7 sigma. > >I'd be interested in hearing how you get on with this approach, off-line if >you prefer. > >Good luck and Happy Christmas! > >Randy Read > >On Dec 24 2009, Peter Grey wrote: > >>Dear Phenix Experts, >> >>I use the SAD+MR option in Phenix. The ASU is huge and the number of >>scatterres is in the few hundreds range. I try to minimize the number of >>runs of Phaser SAD+MR since they take long time on my computer and would >>appreciate your insight regarding the following : >> >> - I noticed that I get much higher signal and much larger number of sites >> if I use density modified phases to calculate the anomalous difference >> map. Is it possible to input these phases instead of the model to Phaser >> ? >> >> - If not, do you recommend providing Phaser with the list of sites found >> in this difference anomalous map. Should such a list include only the >> sites you can be sure of (say above 7 sigma) or all possible sites (say >> above 5 sigma) ? >> >> - Should I use the (peak height)/(sigma of map) as the first estimate of >> occupancy ? if so do I have to normalize it (strongest site has occupancy >> of 1) or can I leave the height/sigma values as they are ? >> >> >>Many thanks, >> >>Peter. >> > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb > >

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Re: [phenixbb] Phaser SAD question
by Kitty Pattridge 24 Dec '09

24 Dec '09

"Randy J. Read" <rjr27(a)cam.ac.uk> wrote: >Dear Peter, > >I'm interested in your observation that you get better signal from an >anomalous difference map computed with density-modified phases than you get >with an LLG map using the MR model. Presumably the density modification >just started from the model phases as well? We've never tried that, so >we'll have to look into that. Unfortunately, you can't at the moment start >the LLG completion with a "model" specified through structure factors, >though this is on our to-do list. > >With the MR+SAD option, because it is iterative, there are sites found in >subsequent cycles (where the information from some of the anomalous >scatterers has become available) and you end up with a set of reliable >sites that can be significantly larger than the set obtained from the first >LLG map. Does your anomalous difference Fourier with density modified >phases give you a larger apparently reliable substructure than the >iterative completion? You could use phenix.emma to compare the two >substructures and see how much they have in common. > >You can indeed give Phaser the set of sites that you got from the anomalous >difference map. One way to choose the cutoff would be to see how deep the >deepest hole is (i.e. how many standard deviations the map goes in the >negative direction), and choose a larger number in the positive direction. >Or you could just use the peaks above 6-7 sigma. > >I'd be interested in hearing how you get on with this approach, off-line if >you prefer. > >Good luck and Happy Christmas! > >Randy Read > >On Dec 24 2009, Peter Grey wrote: > >>Dear Phenix Experts, >> >>I use the SAD+MR option in Phenix. The ASU is huge and the number of >>scatterres is in the few hundreds range. I try to minimize the number of >>runs of Phaser SAD+MR since they take long time on my computer and would >>appreciate your insight regarding the following : >> >> - I noticed that I get much higher signal and much larger number of sites >> if I use density modified phases to calculate the anomalous difference >> map. Is it possible to input these phases instead of the model to Phaser >> ? >> >> - If not, do you recommend providing Phaser with the list of sites found >> in this difference anomalous map. Should such a list include only the >> sites you can be sure of (say above 7 sigma) or all possible sites (say >> above 5 sigma) ? >> >> - Should I use the (peak height)/(sigma of map) as the first estimate of >> occupancy ? if so do I have to normalize it (strongest site has occupancy >> of 1) or can I leave the height/sigma values as they are ? >> >> >>Many thanks, >> >>Peter. >> > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb > >

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Phaser SAD question
by Peter Grey 24 Dec '09

24 Dec '09

Dear Phenix Experts, I use the SAD+MR option in Phenix. The ASU is huge and the number of scatterres is in the few hundreds range. I try to minimize the number of runs of Phaser SAD+MR since they take long time on my computer and would appreciate your insight regarding the following : - I noticed that I get much higher signal and much larger number of sites if I use density modified phases to calculate the anomalous difference map. Is it possible to input these phases instead of the model to Phaser ? - If not, do you recommend providing Phaser with the list of sites found in this difference anomalous map. Should such a list include only the sites you can be sure of (say above 7 sigma) or all possible sites (say above 5 sigma) ? - Should I use the (peak height)/(sigma of map) as the first estimate of occupancy ? if so do I have to normalize it (strongest site has occupancy of 1) or can I leave the height/sigma values as they are ? Many thanks, Peter.

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Re: [phenixbb] phenix GUI freezing during refinement and file naming issues
by John Berrisford 23 Dec '09

23 Dec '09

Dear all. When the GUI freezes on me its a complete freeze with no pop up dialog boxes. This means the job history is not recorded and no results are recorded in the GUI. I'm not sure if this is screensaver or desktop switching related - it only seems to happen randomly - mostly when running long jobs where nothing much happens on the screen, in my experience. I'm also using an nVidia card and an upto date version of the X-server (on my ubuntu 9.10 box). I agree this is a minor issue compared to having a great program which works well. But it does mean that if its easier to use a command line all your hard work with the GUI (and its enhancements) will go to waste... John -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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rotational pseudosymmetry in P61?
by Gabriela Guédez R. 23 Dec '09

23 Dec '09

Hi all, how could i determine the r.m.s.d. and matrix of the NCS operator that relates two molecules in the asymmetric unit in P61? i would like to know whether there is rotational pseudosymmetry in the crystal because i see peaks for two molecules in the kappa=180º SR map. Thanks a lot!

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Autosol problem: Failed to carry out Autosol_scale_and_analyze_mad
by Zheng Zhou 23 Dec '09

23 Dec '09

Dear all I installed phenix nightly builds, dev-256. I have solved structures using molecular replacement. Phenix.refine runs smoothly. Thanks for your great work. When I run some test data using autosol, I met the following error message: ******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked See overall log file and also solve log file (in AutoSol_run_1_/LAST.LOG) ******************************************************************************** The LAST.LOG appears to be empty. I also run the phenix.solve command. Here is the output: ********************************************************************************************* $ phenix.solve binary=/usr/local/phenix-dev-254/build/intel-linux-2.6/solve_resolve/exe/solve SOLVEDIR=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files SYMOP=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files/symop.lib SYMINFO=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files/syminfo.lib CCP4_OPEN=UNKNOWN SOLVE_RESOLVE_MALLOC_MAX=7.48024e+09 /usr/local/phenix-dev-254/build/intel-linux-2.6/solve_resolve/exe/solve: error while loading shared libraries: /usr/local/phenix-dev-254/build/intel-linux-2.6/lib/libimf.so: cannot restore segment prot after reloc: Permission denied ***************************************************************************************************** The libimf.so file is there. I run phenix.solve as superuser, but I still have the same problem. Thanks for your help. Best, Joe

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phenix GUI freezing during refinement and file naming issues
by John Berrisford 22 Dec '09

22 Dec '09

Dear all I've recently been having a few problems with the new phenix GUI freezing during refinement runs on several different systems, most often when I try and do something different on the computer which puts the GUI in the background or on a different desktop. I've seen this problem when running a local copy of phenix on a ubuntu 9.10 system or when running the GUI remotely on a mac connected to our Centos linux cluster. When I switch to a different desktop to get on with doing something else (refine jobs can take a long time) the GUI freezes - although the underlying task runs correctly. The only way out of this problem is to force quit the GUI and then restart it. However, this means that the task isn't recorded in my history and all settings used to run the job are lost from the GUI - the parameter file to run the job does exist though. This also means I lose all the nice molprobibity connections to coot which are really useful. Also if I try to run phenix on the Centos linux cluster when running a local windows system the GUI is so sllloooowwww whenever the GUI tries to open a new window that its unsuable. Has anyone else seen these problems and know a cure? If I run phenix locally on a mac I don't seem to have this problem, but it is nice to run the refine job on our linux cluster so that I can get on with doing something else without it slowing down my mac. On another note, when running phenix refine from the GUI it nicely puts all the files in a folder called "Refine_1" etc... with the number incrementing with each run. So, why are the pdb and mtz file always called "refine_1..." not "refine_2 etc... to match the folder name? This would help with keeping track of files during itterative refinement and model building. It would also stop the problem of having lots of files called "refine_1" loaded into coot when I try to compare models from different refine runs. It would also be useful to be able to be able to add a prefix to the file name / folder name / job name in the GUI so that I could distinguish between different refinement experiments. This is easy to do on the command line.... Thanks and merry christmas John -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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Re: [phenixbb] ncs resolve
by Thomas C. Terwilliger 19 Dec '09

19 Dec '09

Hi Georg, I think that if phenix.find_ncs says No NCS found...you might try ncs_in_type=sites then it is interpreting the sites as parts of chains and is trying to find NCS in those chains, while what you want is for it to interpret these as sites and to find ncs in the sites. So I wonder if you did try adding the keyword ncs_in_type as in: phenix.find_ncs my_sites.pdb my_map_coeffs.mtz ncs_in_type=sites If that failed, then I would suggest trying fewer sites that are more separated: perhaps 3 or 4 sites per monomer, as far apart as possible. If that fails (or maybe as your first try actually), take the entire helix, and make 2 copies A and B, placing them in their appropriate places, and then feed these to phenix with: phenix.simple_ncs_from_pdb my_two_copies.pdb and that may do it for you. All the best, Tom T >> Dear phenix users, >> >> luckily autobuild could solve my SAD problem, but didn´t find any NCS. >> Although the protein is a dimer. I analysed the structure in coot now and >> SSM superposed a homolog protein (just one chain) which (fits quite good) >> on >> chain A and B. I then could find a helix which was built in chain A and B, >> I >> took the 8 corresponding aminoacids from A and B and run: phenix.find_ncs >> overall_best_denmod_map_coeffs.mtz overall_best198206ca155163b.pdb with >> and >> without ncs_parameters.force_ncs=True and didn´t get any solution. >> >> The program gives me an output saying: No NCS found...you might try >> ncs_in_type=sites >> >> Any suggestions whats wrong and a smarter way to do this. >> >> Thanks in advance Georg. >> >> -----Ursprüngliche Nachricht----- >> Von: phenixbb-bounces(a)phenix-online.org >> [mailto:[email protected]] Im Auftrag von Thomas Stout >> Gesendet: Freitag, 18. Dezember 2009 23:56 >> An: PHENIX user mailing list >> Betreff: Re: [phenixbb] queueing systems >> >> >> >> We don't use PHENIX, but we do use several queueing systems on three >> different clusters. >> >> SGE is bulletproof and highly recommended. >> >> Condor has some degree of "evilness" -- especially under Windows. I have >> found it prone to grabbing resources indiscriminately and also being very, >> very resistant to uninstallation. Your mileage may vary. >> >> Certain implementations of "torque" are broken - stay away, or at least be >> very cautious and enter with your eyes open. >> >> Cheers, >> Tom >> >> >> -----Original Message----- >> From: phenixbb-bounces(a)phenix-online.org on behalf of Phil Evans >> Sent: Fri 12/18/2009 2:47 PM >> To: PHENIX user mailing list >> Subject: Re: [phenixbb] queueing systems >> >> >> Dear Nat >> >> We use Sun grid engine >> >> Phil >> >> On 18 Dec 2009, at 18:47, Nathaniel Echols wrote: >> >>> Hi all-- >>> >>> I'd like to hear what kinds of queueing systems people are using for >>> running Phenix on managed clusters. The eventual goal - if feasible - >>> is to add support for submitting jobs directly from the Phenix GUI. >>> Anyone who is interested, please send me (not the list) a brief email >>> describing a) the OS, b) the queueing software, and c) the submission >>> method (i.e. shell script, configuration file, simple command). >>> (Also, anyone who is willing to help test this if and when it becomes >>> available, let me know - I have access to Sun Grid Engine and Condor >>> already, but it's probably going to be difficult to test anything else >>> personally.) >>> >>> thanks, >>> Nat >>> >>> -------------------- >>> Nathaniel Echols >>> Lawrence Berkeley Lab >>> 510-486-5136 >>> NEchols(a)lbl.gov >>> >>> >>> >>> >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> This email (including any attachments) may contain material that is >> confidential and privileged and is for the sole use of the intended >> recipient. Any review, reliance or distribution by others or forwarding >> without express permission is strictly prohibited. If you are not the >> intended recipient, please contact the sender and delete all copies. >> Exelixis, Inc. reserves the right, to the extent and under circumstances >> permitted by applicable law, to retain, monitor and intercept e-mail >> messages to and from its systems. >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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queueing systems
by Nathaniel Echols 18 Dec '09

18 Dec '09

Hi all-- I'd like to hear what kinds of queueing systems people are using for running Phenix on managed clusters. The eventual goal - if feasible - is to add support for submitting jobs directly from the Phenix GUI. Anyone who is interested, please send me (not the list) a brief email describing a) the OS, b) the queueing software, and c) the submission method (i.e. shell script, configuration file, simple command). (Also, anyone who is willing to help test this if and when it becomes available, let me know - I have access to Sun Grid Engine and Condor already, but it's probably going to be difficult to test anything else personally.) thanks, Nat -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 NEchols(a)lbl.gov

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refinement in low resolution
by r n 17 Dec '09

17 Dec '09

Hi I am trying to refine the model in low resolution and there are multimer in the asu. I did rigid body refinement after MR , molecule did not move much and R/Rfree stays 45 % and If I do the overlap between the monomers, rms is 0.06. If I do simulated annealing or any type of refinement (group_adp), Rfree is high and R goes down, but the if do the superposition of the monomer, rms is 1.5 to 1.8. So like to know what kind of refinement is can be done in very low resolution between 5 to 6 ang data? Is it any strict ncs could be possible in phenix that should not move the monomer too much? suggestions are appreciated rn

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B(sol) too high
by Matthew Merski 17 Dec '09

17 Dec '09

I am in the process of solving a series of protein/ligand complex structures and ran the Polygon tool on the series. I noticed that, in general, even when all the other statistics were good, the B(sol) term was a bit too high according to Polygon. (The structures with poorer statistics also had high B(sol) values as well.) Since this is a series of multiple structures of the same protein, should this be a concern for me? And if so, what are typical causes of a high B(sol) value? Matt Merski Shoichet Group UCSF

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