July 2013 - phenixbb - phenix-online.org

inconsistent Rwork/Rfree in outputs
by Michael Thompson 09 Jul '13

09 Jul '13

Hello All, I am getting an output from phenix.refine that is somewhat confusing to me. I have a log file that seems to be reporting inconsistent values for the final Rwork and Rfree. The last line of my log file says: Final R-work = 0.1815, R-free = 0.1912 However, when I check the pdb file from phenix.refine, I see: REMARK Final: r_work = 0.1799 r_free = 0.1952 bonds = 0.012 angles = 1.315 In the log file, I get the following table, which seems to agree with what is in the pdb file. R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.1971 0.1916 1.408780e-01 1.965297e-01 1_bss: 0.1971 0.1916 1.508155e-01 2.122150e-01 1_ohs: 0.1971 0.1916 1.447084e-01 2.026856e-01 1_xyz: 0.1928 0.2001 1.348543e-01 2.162596e-01 1_adp: 0.1929 0.2134 1.006068e-01 1.652532e-01 1_occ: 0.1928 0.2127 9.708801e-02 1.642701e-01 2_bss: 0.1784 0.1978 1.001979e-01 1.536656e-01 2_ohs: 0.1786 0.1982 1.146147e-01 1.876601e-01 2_xyz: 0.1777 0.1959 1.187570e-01 1.899659e-01 2_adp: 0.1952 0.2001 1.109064e-01 1.588435e-01 2_occ: 0.1952 0.1995 1.059382e-01 1.580417e-01 3_bss: 0.1831 0.1888 1.066004e-01 1.508888e-01 3_ohs: 0.1833 0.1890 1.217008e-01 1.855605e-01 3_xyz: 0.1824 0.1897 1.256200e-01 1.855714e-01 3_adp: 0.1876 0.2039 1.027854e-01 1.533022e-01 3_occ: 0.1877 0.2042 9.739524e-02 1.525993e-01 4_bss: 0.1770 0.1931 9.830779e-02 1.515598e-01 4_ohs: 0.1772 0.1933 1.132096e-01 1.824877e-01 4_xyz: 0.1775 0.1933 1.179076e-01 1.860704e-01 4_adp: 0.1911 0.2005 1.074584e-01 1.546149e-01 4_occ: 0.1909 0.1997 1.023003e-01 1.530269e-01 5_bss: 0.1805 0.1895 1.034638e-01 1.506407e-01 5_ohs: 0.1807 0.1895 1.185810e-01 1.828381e-01 5_xyz: 0.1803 0.1899 1.244219e-01 1.801964e-01 5_adp: 0.1893 0.2019 1.072974e-01 1.503622e-01 5_occ: 0.1893 0.2023 1.016701e-01 1.492730e-01 6_bss: 0.1792 0.1915 1.021896e-01 1.490341e-01 6_ohs: 0.1794 0.1915 1.174694e-01 1.798680e-01 6_xyz: 0.1804 0.1926 1.224254e-01 1.830383e-01 6_adp: 0.1952 0.2015 1.118187e-01 1.549205e-01 6_occ: 0.1950 0.2017 1.063759e-01 1.538692e-01 7_bss: 0.1842 0.1922 1.076805e-01 1.529198e-01 7_ohs: 0.1845 0.1918 1.227818e-01 1.857086e-01 7_xyz: 0.1846 0.1917 1.292627e-01 1.856928e-01 7_adp: 0.1885 0.2042 1.071531e-01 1.532154e-01 7_occ: 0.1885 0.2044 1.012764e-01 1.524448e-01 7_bss: 0.1797 0.1952 1.353649e-01 1.556126e-01 7_ohs: 0.1799 0.1952 1.353649e-01 1.556126e-01 I'm wondering why this last line of the log file isn't consistent with the other values that are being reported for R/Rfree? Which numbers should I believe? Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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GUI admin issues
by Yarrow Madrona 09 Jul '13

09 Jul '13

Hello, I have a couple of GUI related questions 1. We recently moved all of our data from one hard drive to another. However, we do not know how to change the directory for all of our projects. The directory is similar but the hard drive is now called tp3home instead of tp2home. We found a .phenix directory that has a file with a list of projects and directories. We updated the directories but this did not make a difference in the GUI. 2. Is there a quick way to specify which ligand or amino acid to remove in the GUI with doing simmulated annealing or better to do manually? Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Re: [phenixbb] omit map for protein-DNA complex
by Wei Shi 08 Jul '13

08 Jul '13

Hi guys, With the help of Tom and Nat, I fixed the errors in my pdb file and could generate the simulated annealing omit map for the protein-DNA complex structure! But when I opened resolve_composite_map.mtz and *_ed.pdb in Coot, I could only see one monomer of the protein in Coot. It should be two dimers of the protein plus two pieces of DNA. And when I opened the *_ed.pdb in pymol, it showed the right thing: two dimers of the protein plus two pieces of DNA. It seems that something in *_ed.pdb file is not recognized by Coot. I don't know whether any of you had this before and would have any suggestions for me. When I opened *_ed. pdb with text file and found out that the word "break" is used instead of "ter" between different chains, so I replaced all "break" with "ter", but this didn't help.... Thank you so much! Best, Wei On Wed, Jul 3, 2013 at 10:36 AM, Wei Shi <wei.shi118(a)gmail.com> wrote: > Hi Nat and Tom, > Thank you so much for your help! I don't know why those C7 atoms are > there.... I just added some nucleotides manually using coot to fit the > density. I am going to delete those C7 atoms in DA and see whether that > would help. Thank you guys so much! > > Best, > Wei > > On Tue, Jul 2, 2013 at 5:22 PM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > >> Okay, this makes sense. Wei, are you trying to model methylated DNA, >> or are those C7 atoms there by accident? >> >> -Nat >> >> On Tue, Jul 2, 2013 at 12:11 PM, Terwilliger, Thomas C >> <terwilliger(a)lanl.gov> wrote: >> > Hi Nat, >> > I think it was the input file. Here is a little piece of it: >> > >> > ATOM 3157 P DA E 8 -56.682 44.723-118.292 1.00 37.45 >> P >> > ATOM 3158 C5' DA E 8 -54.313 44.743-117.204 1.00 40.32 >> C >> > ATOM 3159 O5' DA E 8 -55.729 44.807-117.015 1.00 38.38 >> O >> > ATOM 3160 C4' DA E 8 -53.551 44.795-115.886 1.00 35.58 >> C >> > ATOM 3161 O4' DA E 8 -53.433 46.172-115.429 1.00 32.68 >> O >> > ATOM 3162 C3' DA E 8 -54.164 44.027-114.709 1.00 30.30 >> C >> > ATOM 3163 O3' DA E 8 -53.117 43.597-113.848 1.00 30.92 >> O >> > ATOM 3164 C2' DA E 8 -54.997 45.106-114.029 1.00 18.46 >> C >> > ATOM 3165 C1' DA E 8 -53.974 46.233-114.120 1.00 19.87 >> C >> > ATOM 3166 N1 DA E 8 -52.933 50.956-112.506 1.00 4.27 >> N >> > ATOM 3167 C2 DA E 8 -52.179 49.849-112.633 1.00 5.31 >> C >> > ATOM 3168 N3 DA E 8 -52.515 48.630-113.069 1.00 3.59 >> N >> > ATOM 3169 C4 DA E 8 -53.816 48.619-113.401 1.00 5.26 >> C >> > ATOM 3170 C5 DA E 8 -54.722 49.662-113.344 1.00 5.31 >> C >> > ATOM 3171 C6 DA E 8 -54.237 50.894-112.863 1.00 4.84 >> C >> > ATOM 3172 N6 DA E 8 -55.010 51.981-112.750 1.00 5.38 >> N >> > ATOM 3173 C7 DA E 8 -56.909 56.086-110.227 1.00 2.18 >> C >> > ATOM 3174 N7 DA E 8 -55.973 49.258-113.789 1.00 6.11 >> N >> > ATOM 3175 C8 DA E 8 -55.803 47.992-114.102 1.00 7.27 >> C >> > ATOM 3176 N9 DA E 8 -54.525 47.556-113.888 1.00 8.54 >> N >> > ATOM 3177 OP1 DA E 8 -56.215 43.588-119.122 1.00 44.46 >> O >> > ATOM 3178 OP2 DA E 8 -58.094 44.785-117.853 1.00 32.00 >> O >> > >> > Notice the C7 that is not attached to anything and is not normally part >> of a DA nucleotide. >> > -Tom T >> > >> > On Jul 2, 2013, at 1:07 PM, Nathaniel Echols wrote: >> > >> >> On Tue, Jul 2, 2013 at 9:03 AM, Wei Shi <wei.shi118(a)gmail.com> wrote: >> >>> Below is the error message I got when I ran a plain refinement of the >> same >> >>> PDB file and data file. I also ran phenix.ready-set of the PDB file >> using >> >>> default setting (add hydrogen to model if absent, et al) and generate >> a >> >>> updated PDB file and ran refine again, but still got the same error >> message >> >>> as below: >> >> >> >> This sounds like a bug. Could you please email us off-list with the >> >> PDB file and any existing restraints? (We can fake the data for >> >> testing purposes.) >> >> >> >> -Nat >> > >> > >

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Re: [phenixbb] problem refining Fe-S cluster
by Edward A. Berry 05 Jul '13

05 Jul '13

Pavel Afonine wrote: > Hi Ed, > > it looks like occupancies and B-factors need to be refined and refined > until convergence. Also, if you apply any distance restraints for > clusters (restrain Fe-S distances) make sure these restraints are > correct. I've seen many cases like this and typically refining > occupancy/b-factors and making sure restraints are correct solves the > problem. I've never seen fixing specific parameters help and I can't > understand logic for doing this. > OK. I'm not giving any restraints for the cluster, it must be in the monomers library. I can get SF4.cif from CCP4 and set the weights for bonds/angles very low to let the density rule. But now I see the problem wasn't there a few rounds back, and the difference seems to be that I was using 3 macro_cyles instead of 1. Now I repeat exactly the same refinement both ways, seems to be it. So maybe an artifact of not refining to convergence. Odd though, because it was OK in the starting model, and I'm not asking for the B's to be reset initially to 20 or something. Problem seems to be solved by using the default 3 cycles, but in case anyone is interested, B-factors for Fe are pretty much unchanged after refining 3 cycles B-factors for the Fe's but not the S's, decrease by about 5.0 on refining 1 cycle. Overall and protein B-ave increase on refining 1 cycle Looking at the step by step changes, the first cycle out of 3 is not like the single cycle. This is dev-1420 version of phenix. R-factors refining 3 cycles REMARK R-factors, x-ray target values and norm of gradient of x-ray target REMARK stage r-work r-free xray_target_w xray_target_t REMARK 0 : 0.3205 0.3532 3.857969e+00 3.920754e+00 REMARK 1_bss: 0.2433 0.2823 3.683390e+00 3.779722e+00 REMARK 1_weight: 0.2433 0.2823 3.683390e+00 3.779722e+00 REMARK 1_xyzrec: 0.2457 0.2825 3.689060e+00 3.780966e+00 REMARK 1_adp: 0.2463 0.2823 3.690454e+00 3.780932e+00 REMARK 1_occ: 0.2463 0.2823 3.690455e+00 3.780936e+00 REMARK 2_bss: 0.2463 0.2823 3.690087e+00 3.780536e+00 REMARK 2_weight: 0.2463 0.2823 3.690087e+00 3.780536e+00 REMARK 2_xyzrec: 0.2439 0.2821 3.684528e+00 3.778960e+00 REMARK 2_adp: 0.2434 0.2823 3.683429e+00 3.779315e+00 REMARK 2_occ: 0.2434 0.2823 3.683429e+00 3.779316e+00 REMARK 3_bss: 0.2433 0.2825 3.683615e+00 3.779760e+00 REMARK 3_weight: 0.2433 0.2825 3.683615e+00 3.779760e+00 REMARK 3_xyzrec: 0.2455 0.2825 3.688717e+00 3.780899e+00 REMARK 3_adp: 0.2461 0.2824 3.689934e+00 3.780715e+00 REMARK 3_occ: 0.2461 0.2824 3.689934e+00 3.780714e+00 REMARK end: 0.2457 0.2825 3.689963e+00 3.781089e+00 refining 1 cycle REMARK stage r-work r-free xray_target_w xray_target_t REMARK 0 : 0.3205 0.3532 3.857969e+00 3.920754e+00 REMARK 1_bss: 0.2222 0.2930 3.668217e+00 3.804573e+00 REMARK 1_weight: 0.2222 0.2930 3.668217e+00 3.804573e+00 REMARK 1_xyzrec: 0.2284 0.2941 3.681902e+00 3.808504e+00 REMARK 1_adp: 0.2594 0.3133 3.748285e+00 3.841014e+00 REMARK 1_occ: 0.2594 0.3133 3.748284e+00 3.841012e+00 REMARK end: 0.2692 0.2912 3.759155e+00 3.806820e+00 REMARK ------------------------------------------------------------------------ R B-factors refining 3 cycles REMARK |-----overall-----|---macromolecule----|------solvent-------| REMARK stage b_max b_min b_ave b_max b_min b_ave b_max b_min b_ave REMARK 0 : 90.34 16.23 43.10 90.34 16.23 42.91 80.33 27.29 46.57 REMARK 1_bss: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_weight: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_xyzrec: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_adp: 89.27 16.38 42.96 89.27 16.38 42.79 80.39 26.98 46.24 REMARK 1_occ: 89.27 16.38 42.96 89.27 16.38 42.79 80.39 26.98 46.24 REMARK 2_bss: 89.37 16.47 43.06 89.37 16.47 42.88 80.49 27.08 46.34 REMARK 2_weight: 89.37 16.47 43.06 89.37 16.47 42.88 80.49 27.08 46.34 REMARK 2_xyzrec: 89.37 16.47 43.06 89.37 16.47 42.88 80.49 27.08 46.34 REMARK 2_adp: 89.46 16.19 42.92 89.46 16.19 42.74 80.48 26.86 46.22 REMARK 2_occ: 89.46 16.19 42.92 89.46 16.19 42.74 80.48 26.86 46.22 REMARK 3_bss: 89.63 16.36 43.09 89.63 16.36 42.92 80.66 27.03 46.39 REMARK 3_weight: 89.63 16.36 43.09 89.63 16.36 42.92 80.66 27.03 46.39 REMARK 3_xyzrec: 89.63 16.36 43.09 89.63 16.36 42.92 80.66 27.03 46.39 REMARK 3_adp: 89.22 16.53 42.92 89.22 16.53 42.75 80.45 26.77 46.08 REMARK 3_occ: 89.22 16.53 42.92 89.22 16.53 42.75 80.45 26.77 46.08 REMARK end: 89.22 16.53 42.92 89.22 16.53 42.75 80.45 26.77 46.08 refining 1 cycle: REMARK |-----overall-----|---macromolecule----|------solvent-------| REMARK stage b_max b_min b_ave b_max b_min b_ave b_max b_min b_ave REMARK 0 : 90.34 16.23 43.10 90.34 16.23 42.91 80.33 27.29 46.57 REMARK 1_bss: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_weight: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_xyzrec: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_adp: 85.40 23.38 49.20 85.40 23.38 49.17 81.25 33.88 49.84 REMARK 1_occ: 85.40 23.38 49.20 85.40 23.38 49.17 81.25 33.88 49.84 REMARK end: 85.40 23.38 49.20 85.40 23.38 49.17 81.25 33.88 49.84 REMARK ------------------------------------------------------------------------ R starting model oswego 236% grep SF4 sqr1402e_002.pdb ATOM 8568 FE4 SF4 B1003 15.699 21.265 101.440 1.00 31.53 Fe ATOM 8569 FE1 SF4 B1003 15.302 20.444 104.268 1.00 28.32 Fe ATOM 8570 FE3 SF4 B1003 15.072 18.385 101.975 1.00 30.57 Fe ATOM 8571 FE2 SF4 B1003 17.702 19.420 102.964 1.00 32.57 Fe ATOM 8572 S2 SF4 B1003 14.066 20.264 102.463 1.00 39.50 S ATOM 8573 S3 SF4 B1003 16.963 21.440 103.248 1.00 28.46 S ATOM 8574 S1 SF4 B1003 16.723 19.393 100.994 1.00 31.08 S ATOM 8575 S4 SF4 B1003 16.026 18.425 103.963 1.00 29.56 S refining 3 cycles oswego 235% grep SF4 sqr1402e_006.pdb ATOM 8568 FE4 SF4 B1003 15.708 21.268 101.432 1.00 31.37 Fe ATOM 8569 FE1 SF4 B1003 15.283 20.449 104.291 1.00 28.14 Fe ATOM 8570 FE3 SF4 B1003 15.062 18.373 101.986 1.00 30.15 Fe ATOM 8571 FE2 SF4 B1003 17.720 19.419 102.961 1.00 32.34 Fe ATOM 8572 S2 SF4 B1003 14.080 20.264 102.462 1.00 38.64 S ATOM 8573 S3 SF4 B1003 16.943 21.422 103.257 1.00 28.96 S ATOM 8574 S1 SF4 B1003 16.712 19.383 101.004 1.00 31.27 S ATOM 8575 S4 SF4 B1003 16.036 18.446 103.959 1.00 29.32 S refining 1 cycle oswego 234% grep SF4 sqr1402e_005.pdb ATOM 8568 FE4 SF4 B1003 15.763 21.282 101.383 1.00 26.59 Fe ATOM 8569 FE1 SF4 B1003 15.274 20.434 104.305 1.00 23.38 Fe ATOM 8570 FE3 SF4 B1003 15.026 18.351 102.006 1.00 25.63 Fe ATOM 8571 FE2 SF4 B1003 17.779 19.437 102.902 1.00 27.63 Fe ATOM 8572 S2 SF4 B1003 14.132 20.305 102.437 1.00 34.56 S ATOM 8573 S3 SF4 B1003 16.929 21.408 103.255 1.00 28.42 S ATOM 8574 S1 SF4 B1003 16.681 19.335 101.002 1.00 29.49 S ATOM 8575 S4 SF4 B1003 16.105 18.462 103.923 1.00 28.25 S

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problem refining Fe-S cluster
by Edward A. Berry 05 Jul '13

05 Jul '13

I have a problem refining a structure with iron-sulfur clusters. The irons refine to low B-factors (~25 in this case, while wilson B and B-average are around 45 and the Sg's ligating the irons are ~30). The irons have negative difference density and there is positive density in the center of the cluster (not on the S as it appears; the S is actually above the plane of the irons and the positive density below). (see attached map) It's possible that the cluster is lost in some percent of the molecules, and I could refine occupancy to get rid of the negative density, but I suspect this is likely to be because the B-factors are too low. I will try manually setting B for the Fe's and refining without ADP step, but does anyone have a better suggestion? This was refined for one macrocycle with strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous thanks, eab

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divergence of R and Rfree at the last step of refinement
by Edward A. Berry 04 Jul '13

04 Jul '13

I'm refining a structure with phenix-dev-1414 version, and R-free decreases until the last step where R-work drops sharply and R-free increases. Am I doing something wrong? R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.3068 0.3347 4.111964e+00 4.184576e+00 1_bss: 0.2296 0.2735 3.919523e+00 4.036648e+00 1_weight: 0.2296 0.2735 3.919523e+00 4.036648e+00 1_xyzrec: 0.2377 0.2725 3.938818e+00 4.036514e+00 1_adp: 0.2311 0.2707 3.918953e+00 4.031556e+00 1_occ: 0.2311 0.2707 3.918944e+00 4.031541e+00 end: 0.2187 0.2795 3.907777e+00 4.050961e+00 ////////////////////////////////////////////////////////////////// Looking in the log file, it seems that this happens at the stage of correcting the solvent mask: ============================= updating all scales ============================= start: r_work=0.3152 r_free=0.3389 (reset all scales to undefined) bulk-solvent and scaling: r_work=0.2324 r_free=0.2703 remove outliers: r_work=0.2324 r_free=0.2703 *-> correct solvent mask: r_work=0.2187 r_free=0.2795 <--*** final: r_work=0.2187 r_free=0.2795 overall anisotropic scale matrix: V0: 2.5130,-0.3626,1.3424,-0.7174,-0.0625,-2.3276 V1: -0.0348,-0.0556,-0.0105,-0.0091,0.0085,0.0052

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Very low resolution data set
by Xiang Li 03 Jul '13

03 Jul '13

Hi everyone, I am working on a very low resolution data set (14 A). It is a designed DNA crystal and unit cell size & symmetry fit well with the assumption. When I do the refinement I found the Rfree is extreme high, ~0.49 while Rwork is about 0.4. But the model seems fits in well with the density map. I have collected different datasets, and it gives about the same MR result for different sets. I do not have any experience to work with low resolution data. Here I have a few questions: 1 What is the expected Rfree and Rwork for such low resolution data? I looked up PDB bank, and there is a 11.5A crystal with Rfree=~0.4. But not sure whether there is a kind of value for Rfree to consider the refinement works or not. 2 There might be overfit problem during the refinement. Currently what I did is to optimize the weight with PHENIX gui, add restraints between basepairs and NCS restraint. I tried to manually adjust the weight, but seems the optimized weight gives the best result. Are there other things I should try? 3 How to confirm that the result is real? There will be larger than usual error for such low resolution data, and what the supposed range should be? Thanks a lot for your suggestions and help! Sincerely, Xiang

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omit map for protein-DNA complex
by Wei Shi 02 Jul '13

02 Jul '13

Hi guys, I've been trying to generate the omit map for a protein-DNA complex structure using Phenix. I don't know why it takes forever to run and didn't seem like to finish at all.... The resolution of the dataset is 3.2A. Omit map type: simulated annealing. Omit region: composite. And, for the corresponding apo-protein structure, the simulated annealing omit map was generated within 2 or 3 hours on the same computer cluster. Let me know whether you have any idea about what might go wrong and whether there is anything I could do.... Thank you so much! Best, Wei

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Bias in Rfree
by "Weiergräber, Oliver H." 02 Jul '13

02 Jul '13

Hello, while refining a structure with NCS, I was re-considering this paper from Michael Chapman's group: Fabiola F, Korostelev A, Chapman MS. Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetry. Acta Crystallogr D Biol Crystallogr. 2006 Mar;62(Pt 3):227-38. In essence, they suggest to exclude from the working set reflections that are (1) related to a test reflection by NCS (2) adjacent to a test reflection and its NCS mates in reciprocal space They have implemented this strategy in a CNS module (R-free2005), but the software is no longer actively supported. Does anybody know if something similar has ever been implemented in other software packages such as phenix? Or am I missing any significant downsides of the approach - apart from a reduction of the working set? Best regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Error while updating water
by Subhani Bandara 01 Jul '13

01 Jul '13

Dear all, I am refining a protein structure at 2.5 A. After running some refinements with water update option on, I manually added water to some positions and ran without water update option as it removes those water from the sites and show green density around. Then after some refinements like this, I tried to use water update option to add water to some newly appeared density. When I check the option to update water using dev 1418 version it stops with the following error. Also when not using water update option, refinement statistics got worse when I used 1418 compared to 1.8.2-1309 with refinements using same inputs and options. R work-0.1988 compared to 0.1920 with 1.8.2-1309 Rfree-0.2623 compared to 0.2490 with 1.8.2-1309 Traceback: File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/thread_utils.py", line 236, in run return_value = self._target(self._args, self._kwargs, self._c) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py", line 94, in __call__ result = self.target() File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py", line 73, in __call__ result = self.run() File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py", line 69, in run refine_object = self._run(args, callback) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py", line 85, in _run call_back_handler=callback) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/command_line.py", line 161, in run call_back_handler=call_back_handler) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/driver.py", line 1630, in run ncs_manager = self.ncs_manager).result File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/strategies.py", line 155, in __init__ neutron_refinement2 = self.neutron_refinement2) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 26, in __init__ self.__call__() File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 36, in __call__ self.__getattribute__(method_name)() File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 106, in run_sol mc = self.macro_cycle) File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 79, in _need_to_run else: raise RuntimeError("Not a valid mode: %s"%mode) Thanks in advance for any help Subhani

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