March 2009 - phenixbb - phenix-online.org

Re: [phenixbb] phenix.automr ensemble/component question
by Thomas C. Terwilliger 23 Jul '10

23 Jul '10

Hi Scott, Your first command looks good to me. It is saying that the composition of the crystal is 2 copies of each chain: component_1.component_copies=2 component_2.component_copies=2 and you want to search for 2 copies of each of your search models: ensemble_1.copies_to_find=2 ensemble_2.copies_to_find=2 All the best, Tom T > Hi Phenixers, > > I'm a bit confused about the proper syntax for my phenix.automr job. > This is probably a simple concept, but I'm running on 3 hours of sleep > as my kid was up all night, and my synapses aren't working so good. > > I expect 2 copies of my protein per AU > > My protein is composed of two domains > > I have a single PDB search model for each domain > > is either of these commands correct? > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=2 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=2 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > or > > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=1 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=1 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > essentially I'm not really using an ensemble of search models, I only > have a single PDB for each domain. So should ensemble_1.copies_to_find > and ensemble_2.copies_to_find be set to 1 or 2? > > > Thanks, > Scott > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Scott Classen, Ph.D. > SIBYLS Beamline 12.3.1 > http://bl1231.als.lbl.gov > Advanced Light Source > Lawrence Berkeley National Laboratory > 1 Cyclotron Rd > MS6R2100 > Berkeley, CA 94720 > C) 510.206.4418 > O) 510.495.2697 > Beamline) 510.495.2134 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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optimize_wxc and wxu
by Scott Classen 08 Apr '09

08 Apr '09

Hello phenixbb, In general should one optimize wxc and wxu ONLY as a final polishing step or can this be done earlier in the refinement and then the optimized values used for subsequent rounds of refinement? If so which values in the log file should be written into the .def file and where? Here is a snippit from my def file after I optimized weights and changed the optimize flags back to False: target_weights { mode = *automatic every_macro_cycle wxc_scale = 0.5 wxu_scale = 1 wc = 1 wu = 1 fix_wxc = None fix_wxu = None optimize_wxc = False bonds_rmsd_max = 0.05 angles_rmsd_max = 3.5 optimize_wxu = False shake_sites = True shake_adp = 10 regularize_ncycles = 50 verbose = 1 wnc_scale = 0.5 wnu_scale = 1 rmsd_cutoff_for_gradient_filtering = 3 } Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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imaginary map (anomlous difference Fourier) from phenix
by Ulrich Baumann 06 Apr '09

06 Apr '09

Hi everybody, I used phenix for calculating anomalous Fourier coefficients (script below) and I get the desired file containing columns FANOM PHANOM. When I read this into Coot for displaying the imaginary map, I only get noise, regardless of resolution cutoff etc. When I export the Fcalcs as CNS format and use CNS for the map calculation, I get very high peaks (i.e. excellent signal-to-noise ratio) on the anomalous scatterers. Inspection of the phenix fcalc file reveals that FOFCWT_no_fill equals FANOM and PHFOFCWT_no_fill is identical to PHANOM . Obviously I am doing something stupidly wrong. Setting xray_data.force_anomalous_flag_to_be_equal_to=true doesn't change anything, by the way, and i am using the latest Phenix version. I vaguely remember that there were an issue with anomlous data but can't find the thread. Thank you very much in advance for enlightening me, Ulrich # source /usr/local/phenix-1.4-3/phenix_env phenix.refine m226h1_rfree-unique.mtz m226h1_hkl2000_6_waters_001.pdb main.number_of_macro_cycles=1 \ refinement.input.xray_data.labels="F(+),SIGF(+),F(-),SIGF(-)" \ xray_data.high_resolution =3.5 strategy=none export_final_f_model=cns output.prefix=sfcalc --overwrite * Space group = 'P3121' (number 152) The mapcoeff.mtz looks like OVERALL FILE STATISTICS for resolution range 0.000 - 0.319 ======================= Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 ASC 0 49 0 100.00 23.7 23.7 88.43 1.77 H H 2 NONE 0 28 0 100.00 8.4 8.4 88.43 1.77 H K 3 NONE -69 69 0 100.00 0.6 26.2 88.43 1.77 H L 4 NONE 0.0 2220.8 0 100.00 235.55 235.55 88.43 1.77 F 2FOFCWT 5 NONE -180.0 180.0 0 100.00 2.65 89.99 88.43 1.77 P PH2FOFCWT 6 NONE 0.0 956.4 0 100.00 72.48 72.48 88.43 1.77 F FOFCWT 7 NONE -180.0 180.0 0 100.00 2.16 89.97 88.43 1.77 P PHFOFCWT 8 NONE 0.0 2202.8 117 99.84 234.51 234.51 37.16 1.77 F 2FOFCWT_no_fill 9 NONE -180.0 180.0 117 99.84 2.78 89.99 37.16 1.77 P PH2FOFCWT_no_fill 10 NONE 0.0 961.2 117 99.84 72.39 72.39 37.16 1.77 F FOFCWT_no_fill 11 NONE -180.0 180.0 117 99.84 2.19 89.95 37.16 1.77 P PHFOFCWT_no_fill 12 NONE 0.0 961.2 117 99.84 72.39 72.39 37.16 1.77 F ANOM 13 NONE -180.0 180.0 117 99.84 2.19 89.95 37.16 1.77 P PHANOM No. of reflections used in FILE STATISTICS 72570 1 1 3 88.81 -133.90 400.50 -133.90 139.90 -134.31 502.82 -134.31 502.82 -134.31 1 1 4 719.55 109.38 336.98 109.38 703.51 104.61 304.13 104.61 304.13 104.61 1 1 5 987.30 124.20 664.11 124.20 985.68 119.49 659.96 119.49 659.96 119.49 1 1 6 871.35 35.76 152.79 35.76 894.80 36.84 198.58 36.84 198.58 36.84 1 1 7 425.64 38.73 189.77 38.73 419.88 34.24 177.78 34.24 177.78 34.24 1 1 8 406.00 -154.97 53.51 25.03 416.82 -153.85 32.47 26.15 32.47 26.15 1 1 9 73.73 139.84 441.04 139.84 92.83 139.16 479.45 139.16 479.45 139.16

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Re: [phenixbb] phenixbb Digest, Vol 40, Issue 31
by Marjolein Thunnissen 31 Mar '09

31 Mar '09

> > Hi Marjolein, > >> I have been trying to find in the documentation if there is a way to do this >> but I have the following problem: In a recent structure we are currently >> refining we identified a spermine molecule sitting right on a >> crystallographic two-fold axis. Spermine has internal two-fold symmetry and >> it is part of extensive crystal contacts. I just wonder how to refine this >> with Phenix. In Refmac it is easy, I put the occupancies to 0.5 and the >> program ignores the clashes of the symmetry related molecule, but that >> doesn't seem to be the way that Phenix works. Can anyone give me advise on >> this? > > Supporting the occupancy trick is on my to-do list (fairly high up). > > In the meantime, could you try giving only the asymmetric unit of the > spermine? I.e. delete all duplicate atoms from your pdb file. > The restraints across the symmetry bond will not work automatically. > You have to define a "custom bond" instead, and if you also want to > restrain the angles, custom pseudo-bonds. See the > "Definition of custom bonds and angles" section. > In your case you'll have to define symmetry_operations (not shown > in the docs), e.g.: > > bond { > action = *add > atom_selection_1 = resname SPM and name C7 > atom_selection_2 = resname SPM and name C7 > symmetry_operation = -x,-y,z > distance_ideal = 1.5 > sigma = 0.01 > } > > The main difficulty will be to find the correct symmetry_operation > for each custom bond. If you send my the CRYST1 card from your > PDB file and the part with the SPM residue I could help out. > > Ralf > > > ------------------------------ Hi, The commands worked indeed the trick. Luckily it is actually not that difficult to find the symmetry operators when using coot. One just has to switch drawing symmetry atoms on and clicking on a symmetry atom, coot will tell you in the bottom line which atom it is and which symmetry operator was used to draw it... Thanks again Marjolein __________________________________________________________________________ | Marjolein Thunnissen Phone +46-(0)46-22 24584| | Associate Professor Fax +46-(0)46-22 24692| | Dept of Molecular Biophysics, Lund University http://www.mbfys.lu.se | | PO-Box 124 S-221 00 Lund, Sweden | | | |Scientific coordinator I911 (Max-lab): MAD and fixed-wavelength stations | | for macromolecular crystallography | |__________________________________________________________________________|

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Re: [phenixbb] PHENIX user mailing list <[email protected]>
by Ralf W. Grosse-Kunstleve 30 Mar '09

30 Mar '09

Hi Maia, > I have a Ca2+ ion in a special position. the ocupancy should be 0.5, as > the other half belongs to a symmetry-related molecule. However, > refinement makes the occupansy 1. What should I do to prevent this? > Should not it find automatically that? phenix.refine uses the correct symmetry factor automatically (internally). Unless you have an actual partial occupancy, the occupancy factor in the pdb file should be 1, irrespective of the multiplicity of the special position. Let me know if this doesn't answer your question. Ralf

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can I turn off TLS for subsequent rounds of refinement?
by Scott Classen 30 Mar '09

30 Mar '09

Hi all, As the TLS refinement can take a significant amount of time, I'm wondering if I can turn it off after a few rounds with it on? or will phenix.refine "see" the ANISOU records and assume I am doing anisotropic ADP? Thanks, Scott

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phenix automr
by sbiswas2＠ncsu.edu 30 Mar '09

30 Mar '09

Hi all, I tried to use phenix automr by using the gui and also I am using the latest version of phenix (courtesy of the phenix development team). I asked it to search for two molecules in the asymmetric unit but it finds just one also I am getting negative (-29) LLG value for the final solution. The map also does not look good. I also asked it to search for all possible space group, although I processed the data with P43212 phenix automr finds a different one P41212.Will fixing the space group fix the problem? Does anyone know what is going on? I tried running phaser separately through ccp4 and phaser did find two molecules although the map did not look good in this either. Shya

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Missing map for model
by Folmer Fredslund 30 Mar '09

30 Mar '09

Dear all, In phenix.refine (1.4-3) my electron density maps look weird. I get beautiful density for a helix that is missing from the current model, but absolutely horrible density for the rest of the molecule. Any ideas what is going on? Maps from automr look fine and the density modified map from autobuild also look fine, whereas the autobuild map from refinement has the same features. Any ideas what is going on? I am running all programs with default parameters. Best regards, Folmer Fredslund

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Geometry problem with the ligand
by Jhon Thomas 30 Mar '09

30 Mar '09

Hello all I am working with a 3.0 A dataset, which binds with cAMP. I have refined the dataset with phenix (TLS+Group_adp) and followed by weight optimization. Though cAMP fit well in the density, validation tools (molprobity, procheck) suggest the bond angles and bond lengths of ligand of completely refined model is very bad(100% bad). Can anyone suggest what could be the problem with model or refinement? I will appreciate the suggestions. Thanks in advance John

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weight optimization
by peter hudson 29 Mar '09

29 Mar '09

Hello all I am very new to this field. I am refining a dataset of 3.0A resolution. I want to perform the weight optimization. while weight optimisation, occupancy refinemnet is default. I donot want torefine the occupancy of any of the atoms from my model. How can i set to occupancy_refinemnet=false. I will appreciate the suggestions. Thanks in advance Peter

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