- phenixbb - phenix-online.org

Calculation of RSR for a fragment of PDB
by George Devaniranjan 18 Jun '14

18 Jun '14

Hi everyone, I apologize at the beginning itself as I am new to using PHENIX/X-ray crystallography so this question might not make the most sense but I will try and explain it well. I cut out a part of a map for a PDB fragment using phenix map cut out density resulting in a MTZ file. Now I changed the fragment (changed its phi and psi externally) and want to calculate the RSR [real-space R -factor] for the model based on the old density (to check if I have made things worse or not). how can I go about this? I tried using phenix.refine couldn't get it to work. I have attached the MTZ fragment, the original PDB fragment and the modified PDB fragment. native: nativeFragment.pdb model: modelledFragment.pdb MTZ: cut_out_density.MTZ (I can see mine is worse but I want to quantify that "badness") Thank you, George

2 4

Re: [phenixbb] special positions
by Yarrow Madrona 18 Jun '14

18 Jun '14

Hi Pavel, It turns out I do have some special positions. Waters sit near a 2 fold axis. I have given them 0.5 occupancy. No error comes up but they simply get kicked out of the electron density. Maybe I should turn off rigid body refinement since I don't need it? Below is a link to a screen shot. https://www.dropbox.com/s/lt3hqzjmygin9l8/special_position.png -Yarrow On Wed, Jun 18, 2014 at 8:49 AM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Yarrow, > > oh good! I'm glad you solved the problem -:) > > All the best, > Pavel > > > On 6/18/14, 8:02 AM, Yarrow Madrona wrote: > > Hi Pavel, > > Thanks for your quick response. It turns out that after I reprocessed a > data set in a higher symetry space group I forgot to use a reference mtz so > the orientation was completely off. I just re-ran phaser and everything > worked fine. I didn't run rigid body refinement after phaser. > > The original error message didn't list the atoms and I am not sure how > it could have any atoms on special positions with the solution being > completely wrong. Probably nothing to worry about. > > -Yarrow > > On Tuesday, June 17, 2014, Pavel Afonine <pafonine(a)lbl.gov> wrote: > >> Hi Yarrow, >> >> ok, I wish that error message (that I put a while ago, in 2009 to be >> precise) lists those atoms... Can you send me the file so I can tell you >> what these atoms are? >> >> In general, if at rigid-body refinement stage you have atoms at special >> positions it is unlikely to be right. >> >> Pavel >> >> On 6/17/14, 12:56 PM, Yarrow Madrona wrote: >> >>> Hi, >>> >>> I am trying to do rigid body refinement, however I get an error in >>> phenix telling me that there are atoms at special positions. >>> >>> I am not sure how to determine which atoms are at special positions so >>> that I can exclude them from rigid body refinement. Can someone help me >>> with this? Thank you. >>> >>> -Yarrow >>> >> >> >

1 0

(no subject)
by Orpheus Mandal 18 Jun '14

18 Jun '14

Hi, Is there any way to perform unrestrained refinement on some selected residues in phenix GUI? Thanks, Orpheus

2 1

Rotamer Selection in Low Resolution Data
by Antony Oliver 18 Jun '14

18 Jun '14

Dear Crystallographic Community, Apologies for the cross-posting, but I *do* routinely use programs from all three software packages. I find myself refining a relatively low resolution structure (3.5 Angstrom) - with 8 molecules in the asymmetric unit. Is there a *simple* automated way to place “optimal-fit to electron density" side-chain rotamers into my model? Preferably in an NCS-independant manner? With thanks, Antony. - - - - - - - - - - - - - - - - - - Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ - - - - - - - - - - - - - - - - - - email: antony.oliver(a)sussex.ac.uk<mailto:[email protected]> tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 http://www.sussex.ac.uk/lifesci/oliverlab http://tinyurl.com/aw-oliver - - - - - - - - - - - - - - - - - -

1 0

special positions
by Yarrow Madrona 17 Jun '14

17 Jun '14

Hi, I am trying to do rigid body refinement, however I get an error in phenix telling me that there are atoms at special positions. I am not sure how to determine which atoms are at special positions so that I can exclude them from rigid body refinement. Can someone help me with this? Thank you. -Yarrow

2 1

coot -> fetch pdb & map using EDS
by Murpholino Peligro 17 Jun '14

17 Jun '14

Hi all How to proceed when Coot -> File -> Fetch PDB and Map using EDS does not work?

4 6

strange increase of R/Rfree in the last tow steps of a macrocycle
by Christian Roth 17 Jun '14

17 Jun '14

Dear Phenix-Team, I did a refinement of 5 macrocycles and it worked really well for 4 cycles, but in the last cycle the R/Rfee increased by nearly 1 percent. Specifically in the last ADP refinement. I don't really understand why. Do you have any comments what might be the problem. it seems that the as optimal chosen weight is not the optimal weight at all. I have copied the relevant part of the logfile in. Thanks in advance for your help. Best Regards Christian ----------Individual ADP refinement---------- R-FACTORS <Bi-Bj> <B> WEIGHT TARGETS work free delta data restr 22.88 25.57 2.69 7.305 69.519 0.356 1.056 25.57 27.18 1.61 5.329 75.682 0.005 1.128 24.30 26.40 2.10 6.197 74.591 0.021 1.087 23.56 26.22 2.66 10.610 72.524 0.082 1.065 23.95 27.03 3.08 14.233 73.918 0.165 1.082 23.67 26.53 2.86 15.745 73.489 0.247 1.073 23.55 26.04 2.49 15.268 73.145 0.329 1.067 23.46 26.14 2.68 17.052 73.654 0.412 1.065 23.25 26.16 2.91 17.712 73.655 0.494 1.061 23.17 26.26 3.09 18.359 73.638 0.576 1.061 22.80 26.15 3.35 15.697 72.615 0.659 1.051 22.73 26.19 3.46 15.989 72.549 0.741 1.050 22.63 26.20 3.57 15.613 72.287 0.823 1.048 max suggested <Bi-Bj> for this run: 10.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.0 Best ADP weight: 0.021 Accepted refinement result: 24.30 26.40 2.10 6.197 74.591 0.021 1.087 |-ADP statistics (Wilson B = 38.175)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 22327 10961 22.54 481.16 74.59 0.25 0.84 0.33 | | all(noH): 11454 10961 22.73 481.16 70.40 0.25 0.84 0.33 | | Sol. : 410 0 24.44 104.66 49.01 None None None | | Mac. : 11044 10961 22.73 481.16 71.19 0.25 0.84 0.33 | | Hyd. : 10873 0 22.54 389.64 79.01 None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 22.735 - 68.577: 7910 | 5: 251.946 - 297.788: 42 | | 1: 68.577 - 114.419: 1983 | 6: 297.788 - 343.631: 25 | | 2: 114.419 - 160.262: 941 | 7: 343.631 - 389.473: 19 | | 3: 160.262 - 206.104: 407 | 8: 389.473 - 435.315: 5 | | 4: 206.104 - 251.946: 113 | 9: 435.315 - 481.157: 9 | | =>continue=> | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of anisotropy: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 0.250 - 0.309: 6325 | 5: 0.546 - 0.605: 227 | | 1: 0.309 - 0.368: 1851 | 6: 0.605 - 0.664: 110 | | 2: 0.368 - 0.428: 1094 | 7: 0.664 - 0.723: 49 | | 3: 0.428 - 0.487: 801 | 8: 0.723 - 0.783: 15 | | 4: 0.487 - 0.546: 474 | 9: 0.783 - 0.842: 15 | | =>continue=> | |-----------------------------------------------------------------------------| =========================== Idealize ADP of riding H ========================== r_work=0.2430 r_free=0.2640 r_work=0.2440 r_free=0.2645 ----------X-ray data---------- |--(resolution: 2.20 - 48.79 A, n_refl.=183093 (all), 5.00 % free)-----------| | | | r_work= 0.2440 r_free= 0.2645 coordinate error (max.-lik. estimate): 0.29 A | | | | x-ray target function (ml) for work reflections: 1.088996 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 48.7982 - 6.8296 0.99 5785 298 0.2106 0.2093 2.1338 2.1779| | 2: 6.8296 - 5.4232 1.00 5818 342 0.2291 0.2632 1.8091 1.8784| | 3: 5.4232 - 4.7383 1.00 5733 351 0.1950 0.2248 1.8106 1.9715| | 4: 4.7383 - 4.3053 1.00 5810 297 0.1865 0.2091 1.8418 1.9422| | 5: 4.3053 - 3.9969 1.00 5770 351 0.1947 0.2125 1.7965 1.8123| | 6: 3.9969 - 3.7614 1.00 5854 317 0.2059 0.2273 1.7389 1.8541| | 7: 3.7614 - 3.5730 1.00 5807 315 0.2165 0.2248 1.6958 1.7279| | 8: 3.5730 - 3.4175 1.00 5743 309 0.2116 0.2532 1.6098 1.7535| | 9: 3.4175 - 3.2860 1.00 5844 333 0.2255 0.2873 1.5248 1.6889| | 10: 3.2860 - 3.1726 0.99 5763 329 0.2437 0.2678 1.4283 1.4634| | 11: 3.1726 - 3.0735 1.00 5828 271 0.2467 0.2763 1.2886 1.403| | 12: 3.0735 - 2.9856 1.00 5803 326 0.2456 0.2590 1.179 1.2299| | 13: 2.9856 - 2.9070 1.00 5782 340 0.2506 0.2807 1.1218 1.155| | 14: 2.9070 - 2.8361 1.00 5762 305 0.2575 0.3100 1.0497 1.0718| | 15: 2.8361 - 2.7716 1.00 5892 309 0.2555 0.2665 0.96762 1.1343| | 16: 2.7716 - 2.7127 1.00 5681 293 0.2698 0.3171 0.92297 1.0768| | 17: 2.7127 - 2.6584 0.99 5948 246 0.2877 0.2608 0.86751 0.93978| | 18: 2.6584 - 2.6082 1.00 5814 297 0.2929 0.2990 0.79337 0.80596| | 19: 2.6082 - 2.5617 0.99 5806 266 0.3032 0.3671 0.75287 0.77999| | 20: 2.5617 - 2.5182 1.00 5886 261 0.3065 0.2973 0.73691 0.83083| | 21: 2.5182 - 2.4776 1.00 5777 298 0.3082 0.3174 0.68817 0.79164| | 22: 2.4776 - 2.4395 0.99 5758 274 0.3293 0.3626 0.64915 0.72304| | 23: 2.4395 - 2.4036 1.00 5864 337 0.3385 0.3388 0.62574 0.73292| | 24: 2.4036 - 2.3698 1.00 5791 322 0.3418 0.3387 0.59163 0.66116| | 25: 2.3698 - 2.3377 0.99 5667 329 0.3491 0.3861 0.55553 0.58025| | 26: 2.3377 - 2.3074 0.99 5876 285 0.3572 0.3901 0.55473 0.60051| | 27: 2.3074 - 2.2785 1.00 5813 305 0.3605 0.3906 0.51979 0.59044| | 28: 2.2785 - 2.2511 0.99 5738 303 0.3831 0.3878 0.48079 0.53204| | 29: 2.2511 - 2.2249 0.98 5716 289 0.4042 0.4574 0.49415 0.54579| | 30: 2.2249 - 2.1999 0.98 5810 256 0.4013 0.4243 0.43974 0.41396| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 48.7982 - 6.8296 5785 298 0.83 22.51 0.97 0.01 10.98| | 2: 6.8296 - 5.4232 5818 342 0.80 26.62 0.97 0.01 6.91| | 3: 5.4232 - 4.7383 5733 351 0.84 22.92 1.00 0.01 6.67| | 4: 4.7383 - 4.3053 5810 297 0.86 20.63 1.00 0.01 6.47| | 5: 4.3053 - 3.9969 5770 351 0.85 21.50 1.00 0.01 5.76| | 6: 3.9969 - 3.7614 5854 317 0.84 22.93 1.01 0.01 5.36| | 7: 3.7614 - 3.5730 5807 315 0.83 24.02 1.02 0.01 4.81| | 8: 3.5730 - 3.4175 5743 309 0.81 26.14 1.02 0.01 4.72| | 9: 3.4175 - 3.2860 5844 333 0.77 29.41 0.98 0.01 4.39| | 10: 3.2860 - 3.1726 5763 329 0.75 31.32 1.01 0.01 3.58| | 11: 3.1726 - 3.0735 5828 271 0.77 29.32 1.06 0.01 2.56| | 12: 3.0735 - 2.9856 5803 326 0.79 28.13 1.04 0.01 1.97| | 13: 2.9856 - 2.9070 5782 340 0.79 28.31 1.02 0.01 1.76| | 14: 2.9070 - 2.8361 5762 305 0.76 30.59 1.00 0.01 1.65| | 15: 2.8361 - 2.7716 5892 309 0.75 31.96 0.99 0.01 1.55| | 16: 2.7716 - 2.7127 5681 293 0.76 31.00 0.98 0.01 1.34| | 17: 2.7127 - 2.6584 5948 246 0.75 32.10 1.01 0.01 1.16| | 18: 2.6584 - 2.6082 5814 297 0.76 31.04 1.12 0.01 0.99| | 19: 2.6082 - 2.5617 5806 266 0.74 33.23 1.09 0.01 1.00| | 20: 2.5617 - 2.5182 5886 261 0.74 32.81 1.08 0.01 0.94| | 21: 2.5182 - 2.4776 5777 298 0.73 33.99 1.06 0.01 0.92| | 22: 2.4776 - 2.4395 5758 274 0.68 38.36 1.05 0.01 0.95| | 23: 2.4395 - 2.4036 5864 337 0.68 37.76 1.05 0.01 0.87| | 24: 2.4036 - 2.3698 5791 322 0.68 37.81 1.04 0.01 0.81| | 25: 2.3698 - 2.3377 5667 329 0.66 40.12 1.02 0.01 0.82| | 26: 2.3377 - 2.3074 5876 285 0.66 40.04 1.02 0.01 0.80| | 27: 2.3074 - 2.2785 5813 305 0.64 41.52 1.00 0.01 0.80| | 28: 2.2785 - 2.2511 5738 303 0.61 43.75 0.96 0.01 0.75| | 29: 2.2511 - 2.2249 5716 289 0.61 43.65 1.00 0.01 0.72| | 30: 2.2249 - 2.1999 5810 256 0.62 43.45 0.97 0.01 0.68| |alpha: min = 0.01 max = 0.01 mean = 0.01| |beta: min = 0.67 max = 12.97 mean = 2.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.74| |phase err.(work): min = 0.00 max = 90.00 mean = 31.89| |phase err.(test): min = 0.00 max = 89.95 mean = 31.57| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r_work=0.2440 r_free=0.2645 n_reflections: 183093 start: r_work=0.4676 r_free=0.5197 (reset all scales to undefined) cycle 0: bulk-solvent and scaling: r_work=0.2443 r_free=0.2670 HD scattering refinement: r_work=0.2436 r_free=0.2671 k_h=-0.50 b_h=68.00 cycle 1: bulk-solvent and scaling: r_work=0.2431 r_free=0.2659 HD scattering refinement: r_work=0.2429 r_free=0.2661 k_h=-0.80 b_h=76.00 remove outliers: r_work=0.2429 r_free=0.2661 correct solvent mask: r_work=0.2403 r_free=0.2646 final: r_work=0.2403 r_free=0.2646 n_reflections: 183093 overall anisotropic scale matrix: V0: 0.7884,-1.3407,1.0850,-0.6410,0.0941,-0.9208 V1: -0.0081,-0.0224,0.0112,0.0027,0.0051,0.0136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work <Fobs> <Fmodel> kiso kani kmask 48.786-25.095 95.24 97 3 0.4187 1086.912 945.454 1.000 0.978 0.333 25.084-20.829 96.12 93 6 0.3183 823.323 739.609 1.000 1.069 0.332 20.816-17.332 95.77 128 8 0.2779 830.776 766.444 1.000 0.984 0.330 17.254-14.349 96.37 278 14 0.2092 778.625 740.522 1.000 0.771 0.303 14.321-11.898 98.22 469 29 0.1781 880.823 854.378 1.000 0.825 0.300 11.885-9.873 99.07 806 50 0.1587 839.382 814.201 1.000 0.810 0.300 9.866-8.193 99.54 1447 65 0.1797 706.818 683.600 1.000 0.854 0.300 8.191-6.800 99.78 2564 127 0.2032 565.003 544.081 1.000 0.859 0.275 6.798-5.642 99.96 4380 260 0.2212 465.483 447.550 1.000 0.842 0.270 5.641-4.682 99.85 7661 461 0.1911 532.250 514.206 1.000 0.869 0.225 4.682-3.885 99.91 13619 747 0.1911 546.495 530.277 1.000 0.970 0.220 3.885-3.224 99.84 23640 1298 0.2156 401.920 389.232 1.000 1.053 0.125 3.224-2.675 99.61 41527 2193 0.2543 219.824 208.597 1.000 1.027 0.020 2.675-2.200 99.31 77230 3893 0.3355 120.901 104.169 1.000 1.008 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9148 b_overall=-2.3712 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.4542 0.5034 0.014 1.36 22.3 139.6 58.4 410 0.000 1_bss: 0.2297 0.2604 0.014 1.36 21.8 139.1 57.9 410 0.000 1_settarget: 0.2297 0.2604 0.014 1.36 21.8 139.1 57.9 410 0.000 1_addcbetar: 0.2297 0.2604 0.014 1.36 21.8 139.1 57.9 410 0.000 1_weight: 0.2297 0.2604 0.014 1.36 21.8 139.1 57.9 410 0.000 1_nqh: 0.2297 0.2605 0.014 1.36 21.8 139.1 57.9 410 0.000 1_xyzrec: 0.2249 0.2590 0.006 0.97 21.8 139.1 57.9 410 0.052 1_regHxyz: 0.2250 0.2591 0.006 0.97 21.8 139.1 57.9 410 0.057 1_adp: 0.2316 0.2642 0.006 0.97 21.9 185.5 60.4 410 0.057 1_regHadp: 0.2334 0.2657 0.006 0.97 21.9 185.5 60.4 410 0.057 2_bss: 0.2326 0.2642 0.006 0.97 21.1 184.8 59.7 410 0.057 2_settarget: 0.2326 0.2642 0.006 0.97 21.1 184.8 59.7 410 0.057 2_weight: 0.2326 0.2642 0.006 0.97 21.1 184.8 59.7 410 0.057 2_nqh: 0.2326 0.2642 0.006 0.97 21.1 184.8 59.7 410 0.058 2_xyzrec: 0.2316 0.2632 0.005 0.85 21.1 184.8 59.7 410 0.061 2_regHxyz: 0.2316 0.2632 0.005 0.85 21.1 184.8 59.7 410 0.064 2_adp: 0.2308 0.2605 0.005 0.85 19.8 213.7 61.5 410 0.064 2_regHadp: 0.2310 0.2604 0.005 0.85 19.8 213.7 61.5 410 0.064 3_bss: 0.2307 0.2610 0.005 0.85 18.9 212.8 60.6 410 0.064 3_settarget: 0.2307 0.2610 0.005 0.85 18.9 212.8 60.6 410 0.064 3_weight: 0.2307 0.2610 0.005 0.85 18.9 212.8 60.6 410 0.064 3_nqh: 0.2307 0.2610 0.005 0.85 18.9 212.8 60.6 410 0.064 3_xyzrec: 0.2337 0.2598 0.004 0.83 18.9 212.8 60.6 410 0.057 3_regHxyz: 0.2337 0.2597 0.004 0.83 18.9 212.8 60.6 410 0.060 3_adp: 0.2354 0.2563 0.004 0.83 26.0 194.2 62.6 410 0.060 3_regHadp: 0.2357 0.2564 0.004 0.83 26.0 194.2 62.6 410 0.060 4_bss: 0.2341 0.2571 0.004 0.83 20.0 188.2 56.6 410 0.060 4_settarget: 0.2341 0.2571 0.004 0.83 20.0 188.2 56.6 410 0.060 4_weight: 0.2341 0.2571 0.004 0.83 20.0 188.2 56.6 410 0.060 4_nqh: 0.2341 0.2571 0.004 0.83 20.0 188.2 56.6 410 0.060 4_xyzrec: 0.2328 0.2564 0.004 0.83 20.0 188.2 56.6 410 0.056 4_regHxyz: 0.2328 0.2564 0.004 0.83 20.0 188.2 56.6 410 0.060 4_adp: 0.2344 0.2569 0.004 0.83 19.3 325.3 63.8 410 0.060 4_regHadp: 0.2353 0.2576 0.004 0.83 19.3 325.3 63.8 410 0.060 5_bss: 0.2321 0.2580 0.004 0.83 19.3 324.6 63.1 410 0.060 5_settarget: 0.2321 0.2580 0.004 0.83 19.3 324.6 63.1 410 0.060 5_weight: 0.2321 0.2580 0.004 0.83 19.3 324.6 63.1 410 0.060 5_nqh: 0.2321 0.2580 0.004 0.83 19.3 324.6 63.1 410 0.060 5_xyzrec: 0.2325 0.2588 0.004 0.82 19.3 324.6 63.1 410 0.056 5_regHxyz: 0.2325 0.2588 0.004 0.82 19.3 324.6 63.1 410 0.060 5_adp: 0.2430 0.2640 0.004 0.82 22.7 481.2 70.4 410 0.060 5_regHadp: 0.2440 0.2645 0.004 0.82 22.7 481.2 70.4 410 0.060 end: 0.2403 0.2646 0.004 0.82 22.7 481.2 70.4 410 0.060 ------------------------------------------------------------------------ CPU time actual refinement: 10207.44 ============================== Exporting results ============================== Writing refined structure to PDB file: /y/people/christian/projects/BtGH84/John/phenix/Refine_18/BtGH84activator_refine_18.pdb n_use = 22327 n_use_u_both = 10961 n_use_u_iso = 11366 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 22327 =============================== Detailed timings ============================== Micro-tasks: mask = 0.00 f_calc = 0.00 alpha_beta = 26.67 target = 5.80 gradients_wrt_atomic_parameters = 0.00 fmodel = 0.00 r_factors = 273.36 phase_errors = 132.42 foms = 1.54 TOTAL for micro-tasks = 439.79 NUMBER OF MASK CALCS= 0 Time per interpreted Python bytecode instruction: 1.763 micro seconds Total CPU time: 2.87 hours from_scatterers_fft: 988 calls, 348.82 s gradients_fft: 534 calls, 461.04 s =========================== phenix.refine: finished =========================== # Date 2014-06-16 Time 21:27:40 BST +0100 (1402950460.37 s) wall clock time: 12291.21 s Start R-work = 0.2297, R-free = 0.2604 Final R-work = 0.2403, R-free = 0.2646

2 1

Strange distance in HEM.cif ligands in phenix library
by Yarrow Madrona 16 Jun '14

16 Jun '14

Hello, After validating a PDB for deposition I received a message that the HEME ligand C2D-C3D distance was longer than ideal. It was 1.52 angstroms, while it was 1.35 for C2A-C3A, C2B-C3B and C2C-C3C. The ideal bond length is listed as 1.544 vs. 1.337 for the other bonds in $PHENIX/chem_data/mon_lib/h/HEM.cif Is there a reason for this? If not, I am inclined to edit it. -Yarrow

2 1

Occupancy refinement of secondary conformation doesn't add up to 1.00
by Benjamin Stauch 15 Jun '14

15 Jun '14

Hi Phenix, I do a refinement of a glycoprotein that has a NAG-NAG attached to an Asn. The data set is very high resolution and I am positive there is indication of a secondary conformation of the entire attachement. I modeled a second conformation in Coot and run my refinement, with the "adjust occupancy" option checked. After initially setting both occupancies to 0.5, I am puzzled to see one of the NAGs to be refined to 0.45 (conformer A) and 0.75 (conformer B) occupancy .. For the other NAG, and indeed all amino acid residues, things always add up like they should. Additionally to this, I was wondering if there was an easy option to restrain each conformer of the entire Asn-NAG-NAG group to have uniform occupancies -- i.e. the Asn and both NAGs of conformer A to have identical occupancy. Thanks and best Ben

2 3

Prime and switch crashing
by Oliver Clarke 13 Jun '14

13 Jun '14

Hi all, I’m getting an error running phenix.prime_and_switch_map that I can’t figure out. It crashes shortly after F(model) initialization. The last part of the log and traceback is appended below - if anyone can figure out what I’m doing wrong I’d be very grateful! I’m running dev-1702 on a Mac (not sure whether this is a mac specific issue though). This happens with multiple different pdb/mtz combinations, so I don’t think it is something specific to my files. Best, Oliver. Command: phenix.prime_and_switch_map model_rs6_refine_001.pdb model_rs6_refine_001.mtz debug=true Error: ----------F(model) initialization---------- Twinning will be detected automatically. |--(resolution: 3.00 - 71.59 A, n_refl.=26875 (all), 5.48 % free)------------| | | | r_work= 0.2683 r_free= 0.3402 coordinate error (max.-lik. estimate): 0.58 A | | | | x-ray target function (ml) for work reflections: 5.858242 | |-----------------------------------------------------------------------------| End of input processing Traceback (most recent call last): File "/Applications/PHENIX-dev-1702/Contents/phenix-dev-1702/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/prime_and_switch_map.py", line 160, in <module> run(sys.argv[1:]) File "/Applications/PHENIX-dev-1702/Contents/phenix-dev-1702/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/prime_and_switch_map.py", line 68, in run map_coeffs = fmodel.electron_density_map().map_coefficients( TypeError: electron_density_map() takes exactly 2 arguments (1 given)

2 2