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Keeping the same origin
by Mo Wong 11 Dec '08

11 Dec '08

Hi all, I would like to compare maps from different phasing runs, so it would make my life much easier if I could keep the same origin. I recall this could be done in solve/resolve, but can't seem to find it mentioned in the phenix documentation. Any suggestions? Thanks!

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resolution bins
by Daniele de Sanctis 10 Dec '08

10 Dec '08

Hi, I was wondering how phenix.refine decide the number of resolution bins in which it shows the refinement statistics (R-free, phase error...). In the case I'm working on it prints out only three resolution bins. Thanks d -- Daniele de Sanctis, PhD Macromolecular Crystallography Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

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Question regarding phenix.elbow
by Young-Jin Cho 03 Dec '08

03 Dec '08

Hi I would like to know how I can add H atoms to my ligand, ADP in the protein complex. I was trying to add H atoms to one of my ligand, ADP. When I types "phenix.elbow --final-geometry=test10bcoot_h_refine_001.pdb --residue=ADP --output=model_h", it went on but failed with the following error message: Traceback (most recent call last): File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1201, in <module> run() File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1108, in run molecule = post_process(molecule, options) File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 577, in post_process options, File "/home2/yjcho/phenix-1.3-final/elbow/elbow/utilities/optimisation_manager.py", line 331, in optimisation_manager pre_opt)) File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 857, in WritePDB original_order=original_order, File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 965, in WritePDB2String self.AdjustHydrogenNames() File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 940, in AdjustHydrogenNames if test_name[3]==" ": test_name[3]="0" TypeError: 'str' object does not support item assignment FYI. ADP is names as ADP as a residue name in the pdb file but has different chain names. By the way, I should mention that I used phenix.reduce first for adding H atoms but it was not able to add sugar H's in ADP molecule albeit other residues were fine. Thanks in advance for your help. Best, YoungJin

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Bulk solvent
by csantiag＠cnb.csic.es 03 Dec '08

03 Dec '08

Hi all, I'm refining a protein and after running phenix.refine I always get a bulk solvent refinement cycle at the end of the process. Is there any way to get rid of the last step? ------------------------------------------------------------------------ REMARK stage angl bond chir dihe plan repu geom_target REMARK 0 : 1.007 0.027 0.237 18.975 0.004 4.107 2.7953e-01 REMARK 1_bss: 1.007 0.027 0.237 18.975 0.004 4.107 2.7953e-01 REMARK 1_xyz: 1.844 0.015 0.087 19.502 0.005 4.106 1.9824e-01 REMARK 1_adp: 1.844 0.015 0.087 19.502 0.005 4.106 1.9824e-01 REMARK 2_bss: 1.844 0.015 0.087 19.502 0.005 4.106 1.9824e-01 REMARK 2_xyz: 1.222 0.008 0.075 19.562 0.005 4.107 1.2876e-01 REMARK 2_adp: 1.222 0.008 0.075 19.562 0.005 4.107 1.2876e-01 REMARK 3_bss: 1.222 0.008 0.075 19.562 0.005 4.107 1.2876e-01 REMARK 3_xyz: 1.021 0.005 0.063 19.049 0.004 4.111 1.0306e-01 REMARK 3_adp: 1.021 0.005 0.063 19.049 0.004 4.111 1.0306e-01 REMARK 3_bss: 1.021 0.005 0.063 19.049 0.004 4.111 1.0306e-01 REMARK ------------------------------------------------------------------------ César Santiago Dept of Macromolecules Structure Centro Nacional de Biotecnología, CSIC Campus Cantoblanco 28049 Madrid Spain csantiag(a)cnb.csic.es

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anomalous scatters refinement
by Daniele de Sanctis 02 Dec '08

02 Dec '08

Hi, I'm making some refinement tests with anomalous data and I wanted to try to refine the anomalous contribution. When would it be the best stage when to introduce it? Thanks D -- Daniele de Sanctis, PhD Macromolecular Crystallography Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

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phenix.autobuild- multiple models
by meindert lamers 29 Nov '08

29 Nov '08

Hi all, I am a bit puzzled by an error message I get when trying to run phenix.autobuild. (I am using the latest/final version of phenix: PHENIX VERSION: 1.3 of 11-08-2008) phenix.autobuild data=01.mtz model=3mei_coot.pdb multiple_models=True include_input_model=True \ multiple_models_number=1 n_cycle_rebuild_max=5 This gives me: **************************************** AutoBuild Input failed Sorry, multiple_models is only available with rebuild_in_place **************************************** However, when I run the same commands using an older version of phenix (PHENIX VERSION: 1.3 of 23-03-2008), all runs fine. Any ideas ? Meindert

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R/Rfree from phenix.autobuild
by Graeme Winter 28 Nov '08

28 Nov '08

Hi Folks, Quick question about R/Rfree from phenix - I ran the autobuild and it kindly built pretty much all of the visible residues, and it gave me the following output: SOLUTION CYCLE R RFREE BUILT PLACED 1 1 0.22 0.23 169 169 2 2 0.21 0.23 170 170 3 4 0.22 0.23 170 170 Now, I'm not one to complain about good results, but I did feel that the Rfree looked a little close to the R factor - usually I would expect a difference of maybe 4-5%. Is there a reason for this that I am missing? The model seemed to fit very nicely, closely corresponded to the PDB entry and the waters were pretty good. There is no NCS (one copy in the ASU) and the phases are from SeMet mad data from Autosol. Resolution is ~1.6A, if that is any help. Just noticed this and thought it was interesting. I am used to Arp/wArp for automated tracing, which typically gives a bigger difference... Many thanks, Graeme

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0 for wxc_scale and wxu_scale?
by Michaela Kramer, Biochemisches Inst. 26 Nov '08

26 Nov '08

I am refining a structure with a resolution of 2.1 Angstroem using Phenix. The spacegroup is P 31 2 1 (No. 152) with a twin fraction of 0.37 and twin law -h,-k,l. In the refinement procedure the NCS (4 chains) constraints are on, using individual sites, ADP and occupancy refinement. In the last refinement step, I use the option to optimize the values for wxu_scale and wxc_scale. These values are optimizes to 0 for wxc_scale and close to 0 for wxu_scale (0.2) When I tried this at earlier refinement stages wxu_scale was also here optimized in some refinement macrocycles to 0. Interestingly I obtain better R values (0.1948/0.2184), than without the optimization by using the default values (0.1391/0.2438 Rwork/Rfree). In addition to that the statistics are better: clashscore 14.41 (compared to 25.73 without wxc_scale & wxu_scale optimization), rotamer outliers 2.33% (compared o 4.66%) and Ramachandran favoured (Molprobity). How is it possible that wxu_scale and wxc_scale can be optimized to 0 by having better statistics? The total refinement target is defined as Etotal= wxc_scale x wxc x Exray + wc x Egeom As I understand it, the crystallographic refinement target (Exray) would now not be considered in the refinement procedure. Would this refinement procedure be valid? And how is wxc (output of target weights: x-ray data) defined? Thank you very much for your help Michaela Here is the output belonging to the optimization: Refinement Macrocycle 1 of 3 ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.649809 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 93.128 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.888942 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 85.407 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== Start r_free = 0.2118 scale= 0.0000 total_weight= 0.0000 r_free= 0.2181 0 scale= 1.0000 total_weight= 1.6498 r_free= 0.2336 0 scale= 1.5000 total_weight= 2.4747 r_free= 0.2379 1 scale= 2.0000 total_weight= 3.2996 r_free= 0.2412 2 scale= 0.6667 total_weight= 1.0999 r_free= 0.2297 0 scale= 0.5000 total_weight= 0.8249 r_free= 0.2245 1 scale= 0.4000 total_weight= 0.6599 r_free= 0.2226 2 Best r_free = 0.2181 ================================ ADP refinement =============================== ----------Individual ADP refinement---------- Start r_free = 0.2181 scale= 0.0000 total_weight= 0.0000 r_free= 0.2247 0 scale= 1.0000 total_weight= 0.8889 r_free= 0.2262 0 scale= 1.5000 total_weight= 1.3334 r_free= 0.2293 1 scale= 2.0000 total_weight= 1.7779 r_free= 0.2310 2 scale= 0.6667 total_weight= 0.5926 r_free= 0.2236 0 scale= 0.5000 total_weight= 0.4445 r_free= 0.2221 0 scale= 0.4000 total_weight= 0.3556 r_free= 0.2208 0 scale= 0.3333 total_weight= 0.2963 r_free= 0.2203 0 scale= 0.2857 total_weight= 0.2540 r_free= 0.2195 0 scale= 0.2500 total_weight= 0.2222 r_free= 0.2191 0 scale= 0.2222 total_weight= 0.1975 r_free= 0.2186 0 scale= 0.2000 total_weight= 0.1778 r_free= 0.2183 0 Best r_free = 0.2183 Refinement Macrocycle 2 of 3 ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.737535 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 89.612 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.228155 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 155.392 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== Start r_free = 0.2179 scale= 0.0000 total_weight= 0.0000 r_free= 0.2223 0 scale= 1.0000 total_weight= 1.7375 r_free= 0.2272 0 scale= 1.5000 total_weight= 2.6063 r_free= 0.2310 1 scale= 2.0000 total_weight= 3.4751 r_free= 0.2332 2 scale= 0.6667 total_weight= 1.1584 r_free= 0.2267 0 scale= 0.5000 total_weight= 0.8688 r_free= 0.2258 1 scale= 0.4000 total_weight= 0.6950 r_free= 0.2269 2 Best r_free = 0.2223 ================================ ADP refinement =============================== ----------Individual ADP refinement---------- Start r_free = 0.2223 scale= 0.0000 total_weight= 0.0000 r_free= 0.2228 0 scale= 1.0000 total_weight= 0.2282 r_free= 0.2235 0 scale= 1.5000 total_weight= 0.3422 r_free= 0.2256 1 scale= 2.0000 total_weight= 0.4563 r_free= 0.2275 2 scale= 0.6667 total_weight= 0.1521 r_free= 0.2219 0 scale= 0.5000 total_weight= 0.1141 r_free= 0.2213 0 scale= 0.4000 total_weight= 0.0913 r_free= 0.2207 0 scale= 0.3333 total_weight= 0.0761 r_free= 0.2204 0 scale= 0.2857 total_weight= 0.0652 r_free= 0.2201 0 scale= 0.2500 total_weight= 0.0570 r_free= 0.2197 0 scale= 0.2222 total_weight= 0.0507 r_free= 0.2195 0 scale= 0.2000 total_weight= 0.0456 r_free= 0.2194 0 Best r_free = 0.2194 Macrocycle 2 of 3 ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.157676 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 93.409 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.228399 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 140.390 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== Start r_free = 0.2163 scale= 0.0000 total_weight= 0.0000 r_free= 0.2189 0 scale= 1.0000 total_weight= 2.1577 r_free= 0.2299 0 scale= 1.5000 total_weight= 3.2365 r_free= 0.2340 1 scale= 2.0000 total_weight= 4.3154 r_free= 0.2341 2 scale= 0.6667 total_weight= 1.4385 r_free= 0.2282 0 scale= 0.5000 total_weight= 1.0788 r_free= 0.2255 1 scale= 0.4000 total_weight= 0.8631 r_free= 0.2249 2 Best r_free = 0.2189 ================================ ADP refinement =============================== ----------Individual ADP refinement---------- Start r_free = 0.2189 scale= 0.0000 total_weight= 0.0000 r_free= 0.2218 0 scale= 1.0000 total_weight= 0.2284 r_free= 0.2231 0 scale= 1.5000 total_weight= 0.3426 r_free= 0.2250 1 scale= 2.0000 total_weight= 0.4568 r_free= 0.2272 2 scale= 0.6667 total_weight= 0.1523 r_free= 0.2215 0 scale= 0.5000 total_weight= 0.1142 r_free= 0.2209 0 scale= 0.4000 total_weight= 0.0914 r_free= 0.2201 0 scale= 0.3333 total_weight= 0.0761 r_free= 0.2197 0 scale= 0.2857 total_weight= 0.0653 r_free= 0.2195 0 scale= 0.2500 total_weight= 0.0571 r_free= 0.2193 0 scale= 0.2222 total_weight= 0.0508 r_free= 0.2191 0 scale= 0.2000 total_weight= 0.0457 r_free= 0.2190 0 Best r_free = 0.2190 Michaela Kramer PhD student Institute of Biochemistry Winterthurerstrasse 190 8057 Zuerich Switzerland

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trouble in phenix.refine
by Huiying Li 26 Nov '08

26 Nov '08

I was running phenix.refine in tls mode with the following command line: phenix.refine mydata.mtz mymodel.pdb strategy=tls tls_group_selection.param mylibrary.cif against a 2.1A data set, P21211 SG, a homodimer in AU, totally 10 tls groups. The following errors occured and program stopped. I do not know how to fix the problem. Traceback (most recent call last): File "/usr/local/phenix-1.3-final/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line 68, in run log=log) .... ... .... File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/monomer_library/pdb_interpretation.py", line 970, in get_lib_link atom_dicts[angle.atom_3_comp_id].get(angle.atom_id_3, None)] IndexError: list index out of range Your help is highly appreciated. Huiying -- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: hli(a)uci.edu

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twin axis for p21
by HUA YUAN 25 Nov '08

25 Nov '08

Dear Colleagues, I'd like to share with you with a twinning puzzle that's been troubling me for a while. I have a ~2.2 A data merged in p212121 space group with unit cell: 41.8300 117.4490 134.4840 90.0000 90.0000 90.0000 Translational NCS was detected but structure solution was able to be obtained by phased molecular replacement as we have a Au derivative data set. Obtaining experimental phase or MR alone didn't work. However, with this model and data set, the refinement didn't work (with R-free ~40% or higher if with more cycles). Different twinning tests have been carried out and no sign of twinning. All possible p222 space groups have been tried but no luck or even worse. Considering that translational symmetry and perfect twinning may make things deceiving, the data was merged into p21 and a twin-refinement was performed in phenix.refine. After 3 cycles of rigid-body and group ADP, a R-free of ~30% was obtained and the output map looks OK. It looks like we got it. But then things get interesting when we tested other two axis as the p21 unique axis. With all the three choices plus corresponding twin-refinement, we could get a similar R-free (30%). Besides, the three maps all look OK except for one missing some side chains. Then the structure was solve in p1 and Xtriage was used with the hope that one axis would stand out. However, the RvsR for all three axis are almost the same. Did I miss anything here? Of course, we could pick up the one axis we like best and get the structure solved ^---^. However, this puzzle would eat me alive for a very long time. Best, Hua

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