Search results for "look through"

[phenixbb] Re: Simulate map from model

by Alexandre OURJOUMTSEV

Hi everybody, Inversely to what Pavel wrote, just if you want to get a limited-resolution map of the Coulomb potential (and not anything else), eventually with a resolution that varies over the map regions, Section 5.2 of the manuscript https://arxiv.org/abs/2412.14350 exactly explains how to do this. I guess, if this critical, Phenix teams can routinely add such an option. With best wishes, Sacha Urzhumtsev De : Pavel Afonine <pafonine(a)lbl.gov> Envoyé : mercredi 2 avril 2025 20:54 À : James Holton <jmholton(a)lbl.gov>; phenixbb(a)phenix-online.org; ricardorighetto(a)gmail.com Objet : [phenixbb] Re: Simulate map from model Hi, additionally: - If you want an exact map (not a finite-resolution Fourier map), use: phenix.model_map model.pdb scattering_table=electron - We are close to making a multipolar model available for density calculations, which—if I understand correctly—is what you need to simulate Coulomb potential maps. This feature is not yet available to general Phenix users, but if you send me the model off-list, I can generate and send the map back to you. Pavel On 4/2/25 10:52, James Holton wrote: Ostensibly, all you need to do is run phenix.fmodel with scattering_table=electron . And perhaps try to come up with what k_sol should be for the bulk solvent density. There are caveats, of course, not the least of which is that, last I checked, the modified scattering from formal charges like ions vs neutral groups is not implemented. I don't actually know of a program that handles things like charges. I've heard rumors that someone was working on full QM calculations of electrons moving through matter to try and get this "right", but I have not heard about any progress for some time. Sorry can't be more helpful, -James On 4/2/2025 4:52 AM, Ricardo Righetto wrote: Hi, Apologies if I'm missing something obvious, but I was not able to find this in the documentation: is there a PHENIX tool for simulating Coulomb potential maps (aka "cryo-EM maps") from atomic models? I'm looking for something like the molmap<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html> command in ChimeraX, but more accurate. One such alternative is the simulate program from cisTEM, but I figured PHENIX might also have something? Thank you! -- Ricardo Diogo Righetto _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org<mailto:[email protected]> To unsubscribe send an email to phenixbb-leave(a)phenix-online.org<mailto:[email protected]> Unsubscribe: phenixbb-leave@%(host_name)s _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org<mailto:[email protected]> To unsubscribe send an email to phenixbb-leave(a)phenix-online.org<mailto:[email protected]> Unsubscribe: phenixbb-leave@%(host_name)s

10 months, 1 week

Re: [phenixbb] Problems placing second component in Phaser

by Morten Groftehauge

Hi Gabor, Sounds good but I was hoping for something I could tell phenix.mr_rosetta that would allow it to find a good second solution. Phenix insists on rerunning place model even if you tell it that the model is already placed. So instead of continuing with the placement that worked I end up with one chain based on my original model another one scattered all over the place... I'll try with AMPLE and see what happens there. Cheers, Morten On 18 February 2013 13:01, Gabor Bunkoczi <gb360(a)cam.ac.uk> wrote: > Hi Morten, > > this is weird. One way around is to manually superpose the mr_rosetta > model onto the original in the full solution, and just do a refinement with > Phaser (you can (kind of) do this automatically by running MRage with both > models). Another idea is to decrease the rotation peak cutoff when finding > the second molecule (PEAKS ROT CUTOFF keyword). > > BW, Gabor > > > On Feb 18 2013, Morten Groftehauge wrote: > > Hi guys, >> >> So I have a solution that covers some of target and I ran it through >> phenix.mr_rosetta and I am actually kinda happy with the output from >> there. >> However, while I can place both (NCS=2) with the original model I only >> seem >> to be able to place one of the rosetta models, even with 'packing >> function' >> set to 'all' or 'allow'. >> Original model - >> Refinement after placing component 1: LLG 175 >> Refinement after placing component 2: LLG 620 >> Rosetta model (packing 'all') - >> Refinement after placing component 1: LLG 295 >> Refinement after placing component 2: LLG 390 >> Rosetta model (packing standard) - >> Refinement after placing component 1: LLG 295 >> Refinement after placing component 2: LLG 350 >> >> More notably there is little to no increase in TFZ with the placement of >> the second component... >> >> There are more residues in the Rosetta model and I would expect more >> clashes but this looks weird. >> >> Cheers, >> Morten >> >> >> > > ______________________________**_________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/**mailman/listinfo/phenixbb<http://phenix-online.org/mailman/listinfo/phenixbb> > -- Morten K Grøftehauge, PhD Pohl Group Durham University

12 years, 11 months

Re: [phenixbb] phenix refinement of cryoEM data

by Pavel Afonine

Hello, > I am a relative newcomer to Phenix. I have a large multimeric protein > structure docked into an electron density map, and I would like to > further refine it by rigid-body refinement using Phenix. Is this a > realistic strategy? yes, this is a perfectly valid intent. Have a look at https://www.dropbox.com/s/imv2yzwodik13in/afonine_etal_wcpcw2015.pdf?dl=0 that overviews and summarizes Phenix refinement tools for cryo-EM. > I have made some attempts, first by converting the .mrc map file to > .mtz as outlined here: > https://www.phenix-online.org/documentation/reference/map_to_structure_fact… If you follow the above link you will see that it is best to refine the model directly against the map (in real space, that is), instead of taking a "detour" through reciprocal space. So my suggestion to you is: - get latest Phenix from nightly builds (it is essential that you use recent Phenix): http://phenix-online.org/download/nightly_builds.cgi - run phenix.real_space_refine (sorry, no GUI yet!): phenix.real_space_refine model.pdb map.ccp4 If you expect the model to make large movements to fit the map, you can enable morphing or/and rigid-body, and also increase number of refinement cycles: phenix.real_space_refine model.pdb map.ccp4 run=minimization_global+rigid_body+morphing macro_cycles=10 > Then I tried to refine using rigid body refinement in Phenix. However, > the program quits but doesn’t really tell me why. Here’s the last part > of the log file: > > Number of unique models: 24 > Time building chain proxies: 36.85, per 1000 atoms: 0.26 > Number of scatterers: 142296 > At special positions: 0 > Unit cell: (342, 342, 342, 90, 90, 90) > Space group: P 1 (No. 1) > Number of sites at special positions: 0 > Number of scattering types: 4 > Type Number sf(0) > S 264 16.00 > O 27720 8.00 > N 25872 7.00 > C 88440 6.00 > sf(0) = scattering factor at diffraction angle 0. > > Writing MTZ file: > /Users/xxx/Documents/Phenix/TEST/Refine_1/Test_refine_data.mtz > > Sorry > > > Can anyone give me any ideas as to what went wrong? Still, I would like to debug this.. Could you please send me the following files: - original map; - MTZ file that you get as result of conversion of this map into structure factors and the command you use to do this; - input PDB file with the model; - phenix.refine command (or GUI setup: .eff file and .log file) that crashes with the above error message. All files will handled confidentially. Files may be large, so please use Dropbox or any similar file sharing utilities. > Also, is there a better way to do this? Yes, see suggestions above! Please let me know if you have any questions or need any help! Pavel

10 years, 9 months

Re: [phenixbb] Using the Same Test Set in AutoBuild and Phenix.Refine

by Thomas C. Terwilliger

Hi Dale, Can you try something else: phenix.refine AutoBuild_run_12_/overall_best.pdb \ refinement.input.xray_data.file_name=\ AutoBuild_run_12/exptl_fobs_freeR_flags.mtz \ refinement.main.high_resolution=2.2 refinement.main.low_resolution=20 \ /usr/users/dale/geometry/chromophores/bcl_tnt.cif This differs from your run only by substituting AutoBuild_run_12/exptl_fobs_freeR_flags.mtz for your 2 refinement data files. This is the exact file that is used in refinement by AutoBuild. I agree that you should be able to use your original data file instead. A possible reason why this has failed is that the original data file has a couple reflections for which there is no data...and which were tossed by AutoBuild before creating exptl_fobs_freeR_flags.mtz . Two files that differ only in reflections with no data will still give different checksums, I think. All the best, Tom T > Hi Dale, > >>> 1) Why you specify reflection MTZ file twice in phenix.refine script? >>> >>> >> I put the mtz in twice because if I put it in once phenix.refine >> complains that I have no free R flags. It seems to want one file with >> the amplitudes and another with the flags. Since I have both in the >> same file I put that file on the line twice and phenix.refine finds >> everything it needs. >> > > phenix.refine looks for free-R flags in your main data file > (1M50-2.mtz). Optionally you can provide a separate file containing > free-R flags (I have to write about this in the manual). However, if > your 1M50-2.mtz contains free-R flags then you don't need to give it > twice. So clearly something is wrong at this step and we need to find > out what is wrong before doing anything else. Could you send the result > of the command "phenix.mtz.dump 1M50-2.mtz" to see what's inside of your > data file? Or I can debug it myself if you send me the data and model. > >> If the MD5 hash of the test set depends on the resolution then >> certainly >> I could be in trouble. > > No. It must always use the original files before any processing. > >> Does the resolution limit affect the MD5 hash of the test set? >> > > No. If it does then it is a very bad bug. I will play with this myself > later tonight. > >> >>> 3) Does this work: >>> >>> (...) >> >> I'll try these but it will take a bit of time. >> > > Don't run it until completion. Just make sure it passed through the > processing step. > > Pavel. > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

18 years, 1 month

Re: [phenixbb] ordered solvent - parameters?

by Pavel Afonine

Hi Mark, phenix.refine finds potential water peaks looking at mFo-DFc map (primary map). Then it sorts these peaks by the distances (water-water, water-other). Then it checks for hydrogen bonding. Finally, it verifies that the peaks are present at 2mFo-DFc map (secondary map) at given sigma. Finally finally, the water B-factors (and occupancies, if requested) are refined separately from refinement of other parameters in order to get a reasonable starting point for the next refinement macro-cycle. The procedure is smart enough about cases when your structure has explicit hydrogen atoms. What is crucial is that this procedure is built into refinement, so the water molecules are updated (added / removed / refined) during refinement and NOT as a separate step. There are various options to refine water with isotropic or anisotropic B-factors, refine water occupancies, etc. We still need to do a better job on NOT picking water into ligand density. This is in our to-do list and will be done at some point. There are a few slides in one of the most recent phenix.refine presentation that outline most of what I wrote above: http://cci.lbl.gov/~afonine/aca2008_knoxville_neutron/phenix_refine_2008_ma… Please let us know if you have any other questions, Pavel. On 7/31/2008 2:03 PM, Mark Collins wrote: > Hi All > > I was just going through the .help section and website documentation > for ordered_solvent. And wonder if somebody could enlighten me as too > the meanings of; > > ordered_solvent { > primary_map_type = mFobs-DFmodel > secondary_map_type = 2mFobs-DFmodel > h_bond_min_mac = 1.8 > h_bond_min_sol = 1.8 > h_bond_max = 3.2 > } > peak_search { > map_next_to_model { > use_hydrogens = False > } > max_number_of_peaks = None > peak_search { > peak_search_level = 1 > max_peaks = 0 > interpolate = True > min_distance_sym_equiv = None > general_positions_only = False > min_cross_distance = 1.8 > } > > What is the difference between the primary and secondary map? Is there > away to pick sites in one and remove in another? Eg. pick sites at 3 sigma > in FoFc and remove if 1.2 sigma in 2FoFc. > > I thought h-bonding was generously about 2.4-3.6A so why the 1.8 and 3.2 > defaults? Also if use_hydrogens = True, does the refinement use h_bond > parameters instead of model_peak_dist and peak_peak_dist parameters, or > both? Also what do all of the peak_search parameters do? > > And finally does anyone have any recommendations for progessively changing > the ordered_solvent parameters? In CNS we used to gradually lower the > 2FoFc peak picking (and deleting) and increase the bfactor_max for > deleting? > > Thanks Mark > > > > ------------------------------------------------------------------------ > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

17 years, 6 months

Re: [phenixbb] TRIED resolve ...NEED A BIGGER VERSION... message

by Felix Frolow

Tom, does it mean that for structure of ANY size the right version of RESOLVE will be activated now automatically? If it does, it is very important improvement FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfrolow(a)post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Jan 5, 2009, at 5:25 PM, Tom Terwilliger wrote: > Hi Ben, > Yes, that is just FYI. There are a few sizes of resolve and this > means the smallest wasn't big enough. I'll change the message so > that it is more informative... > All the best, > Tom T > > > > Thomas C. Terwilliger > Mail Stop M888 > Los Alamos National Laboratory > Los Alamos, NM 87545 > > Tel: 505-667-0072 email: terwilliger(a)LANL.gov > Fax: 505-665-3024 SOLVE web site: http:// > solve.lanl.gov > PHENIX web site: http:www.phenix-online.org > ISFI Integrated Center for Structure and Function Innovation web > site: http://techcenter.mbi.ucla.edu > TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB > CBSS Center for Bio-Security Science web site: http://www.lanl.gov/ > cbss > > > > > On Jan 5, 2009, at 8:09 AM, Ben Eisenbraun wrote: > >> >> Howdy Phenixians, >> >> One of my users is running phenix.autobuild, and while it seems to >> run >> okay, the output contains this warning: >> >> TRIED resolve ...NEED A BIGGER VERSION... >> >> Looking through phenix/phenix/autosol/run_resolve.py, it seems like >> this >> is an informational message, but I'm not sure, so I figured I'd ask. >> >> Is this actually an error? >> >> This is phenix-1.3-final on OS X 10.5. >> >> Thanks. >> >> -ben >> >> -- >> Ben Eisenbraun >> Structural Biology Grid Harvard Medical >> School >> http://sbgrid.org http://hms.harvard.edu >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb

17 years, 1 month

Re: [phenixbb] rotamers

by Kendall Nettles

We have been doing a lot of parallel refinements where we are checking out the new options in PHENIX refinement, and one of the things we have observed is that sometimes the sidechains with no clear electron density end up in the main chain density, and distort the model. There is no clear pattern as to which options lead to this phenotype, as different combinations give different results. Until we can sort out what is causing this, it seems clear to me that it is better to delete the side chains. If you want to leave a side chain with no clear electron density, you have to make sure each one is not distorting the model. So leaving the side chains with no clear electron density requires much work, with a benefit that is not clear to me. Kendall Nettles On Mar 28, 2011, at 1:04 PM, Ed Pozharski wrote: > Pavel, > >> - what you mean by "no density", > > Lack of confidence in placement of the side chain. Everyone would have > somewhat different take on it, but the question is more about what to > do, not how to decide if the side chain is disordered. > >> Therefore this raises another item for your questionnaire: > > There is "other" option, feel free to use it > >> refine group >> occupancy for these atoms (one occupancy per all atoms in question - the >> occupancy typically will refine to something less than 0.5 or so). > > This raises an entirely different question regarding reliability of > occupancy refinement in general due to its correlation with the > B-factors. Another can of worms. > >> This trick with smearing out an atom by B-factor may only work for >> isolated (single) atoms such as waters because they are not bonded to >> anything through restraints. > > Certainly, presence of restraints makes the B-factor increase less > steep. I just looked at an instance of a disordered arginine (no > density above 1 sigma for any side chain atoms), and B-factors jump from > 30 at the backbone to 90 at the tip of the side chain. This would > reduce the density level ~5x, which is probably quite sufficient for > blending it into the solvent. There could be a bit of a problem in the > middle, where B-factors are inflated/deflated, but it does take care of > density reduction. > > Things like atom-specific restraints and modified restraint target may > be of some help, but the effect on the final model may be too small to > validate the effort. > > -- > "I'd jump in myself, if I weren't so good at whistling." > Julian, King of Lemurs > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

14 years, 10 months

Re: [phenixbb] High B-factors after Phenix restrained refinement

by Pavel Afonine

I agree, it is a matter of convention. The total ADP is: Utotal=Ucryst+Ugroup+Ulocal. You can either output the total Utotal into ATOM/ANISOU records or keep Ucryst+Ugroup in REMARKs and output Ulocal into ATOMs. Both ways are valid as long as they yield identical Utotal. For more relevant information, summary and some review, see: - pages 23-29 here: http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf - article "On atomic displacement parameters (ADP) and their parameterization in PHENIX" here: http://phenix-online.org/newsletter/ Pavel On 12/16/11 8:11 AM, Steiner, Roberto wrote: > Hi Da > > Even if you deposit a structure refined with Refmac the PDB now > expects the total B values being present. Have a look at > http://deposit.rcsb.org/adit/REFMAC.html > > What you call "more" correct does not really make much sense to me if > I understand you properly. If you follow the link given above (or use > TLSANL directly from the CCP4) and get 'total Bs' from Refmac I am > sure they will be more or less the same and the Bs from phenix.refine. > > R > > > On 16 Dec 2011, at 15:54, Da Duan wrote: > >> Hi Nat >> >> I was just looking at the average B in the refinement log files from >> Refmac and Phenix Refine. Thanks for the clarification on how Refmac >> and Phenix calculate the average B. My next question is when >> depositing the structure, is it more common to deposit structures >> with the "residual" B-factors or B-factors generated by Phenix that >> includes the TLS and Ucryst contribution? I also performed sfcheck >> and the average B generated by the Wilson plot is ~100 which seems to >> suggest that the Phenix average B is probably "more" correct? >> >> Thanks again >> >> Da >> >> >> >> On Fri, Dec 16, 2011 at 12:31 AM, Nathaniel Echols <nechols(a)lbl.gov >> <mailto:[email protected]>> wrote: >> >> On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <2dd13(a)queensu.ca >> <mailto:[email protected]>> wrote: >> > I used Phenix AutoMR to solved a structure to 3.3A and after 1 >> round of >> > rigidbody refinement with Phenix Refine I proceeded to restrained >> > refinement. The R/Rfree from the refinement decreased nicely as >> expected but >> > the B average is at ~100 (using Group B factor refinement >> option). I took >> > the same model and mtz through Refmac and the B average is >> about ~40. Has >> > anyone experienced this before? I am almost positive it maybe a >> setting >> > issue in Phenix Refine that i should be looking at to get the B >> factors to >> > refine correctly. >> >> How are you calculating the average B? Refmac prints "residual" >> B-factors in the B column of ATOM records - these do not include the >> contribution from TLS and Ucryst (an overall B-factor for the entire >> crystal). In Phenix, the ATOM records always have the total >> isotropic >> B-factor, and this will always be higher than the equivalent in >> Refmac. So it's quite likely that both programs are correct, they're >> just reporting very different things. (And for what it's worth, a >> mean B-factor of 100 is totally normal at 3.3A resolution.) >> >> -Nat >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> >> <ATT00001..c> > > Roberto Steiner, PhD > Randall Division of Cell and Molecular Biophysics Group Leader > King's College London > > Room 3.10A > New Hunt's House > Guy's Campus > SE1 1UL, London, UK > Tel 0044-20-78488216 > Fax 0044-20-78486435 > roberto.steiner(a)kcl.ac.uk <mailto:[email protected]> > > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

14 years, 1 month

Re: [phenixbb] phenix autobuild question

by aberndt＠mrc-lmb.cam.ac.uk

Hi Tom, thanks for your answer. I just checked the phenix version I used and it is version-1.3-final. Please find attached the .log file you asked for. I just realised that resolve apparently had a problem with the .mtz label assignment. I never had this problem before. Now that I mention that I have to confess that this is not entirely true. All the phenix tutorials I have looked through so far state that you can use ccp4s mtz the way they are. Yet, this is not entirely true. Say I want to have an analysis from phenix.xtriage by typing 'phenix.xtriage latest.mtz'. So phenix will give me the error message: Multiple equally suitable arrays of observed xray data found. Possible choices: ab_xds_pointless_scala5.mtz:IMEAN_XDSdataset,SIGIMEAN_XDSdataset ab_xds_pointless_scala5.mtz:I_XDSdataset(+),SIGI_XDSdataset(+),I_XDSdataset(-),SIGI_XDSdataset(-),merged Please use scaling.input.xray_data.obs_labels to specify an unambiguous substring of the target label. Sorry: Multiple equally suitable arrays of observed xray data found. Is there a way a way to avoid going back to ccp and sorting the labels accordingly. What would be the 'scaling.input.xray_data.obs_labels' command in the xtriage command line? Anyway, Tom, many thanks for your answer in advance! I reaaly like working with phenix. I just need to learn loads more ... Best, Alex > Hi Alex, > > I'm sorry for both the failure and the lack of a clear message here! I > will try to fix both. > > Is this running phenix-1.3-final? (If not, could you possibly run with > that version so we are on the same version.) > > Can you possibly send me the end of the output in > > /someplace/home/someuser/ > work/someproject/phenix2/AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/AutoBuild_run_1_1.log > > which I hope will have an actual error message to look at? > > The reason for the subdirectories is this: phenix.autobuild runs several > jobs in parallel (if you have set nproc ) or one after the other (if you > have not set nproc). These subdirectories contain those jobs...which are > then combined together to give the final results in your overall > AutoBuild_run_1_/ directory. > > I don't know the answer to the phenix.refine question...perhaps Pawel or > Ralf can answer that one. > > All the best, > Tom T > >> Dear phenix community, >> >> I started an AutoBuild run using the phenix GUI (ver 1.3 rc4) on a >> linux cluster. It worked okay and all the refinement looked pretty >> decent. However, after quite a while I obtained the following error >> message (see below). Would anyone please tell me what to do to prevent >> this error and get phenix get its job finished? >> >> Also, I don't understand why phenix AutoBuild creates 5 (or whatever >> number) AutoBuild_run_x in the AutoBuild-run_1/TEMP0 directory and not >> two dirs up in the tree. In other words in my /someplace/home/someuser/ >> work/someproject/phenix2/AutoBuild_run_1_/TEMP0 directory are more >> AutoBuild_run_x_ directories (with x=1 to 5). It is a bit confusing to >> me. >> >> A final question: I realised that the phenix.refine drastically >> increases the number of outliers. I know that thare is a weighting >> term someplace ... but what was it again? >> >> Many thanks in advance, >> Alex >> >> >> warnings >> Failed to carry out AutoBuild_multiple_models: >> Sorry, subprocess failed...message is: >> ******************************************************************************** >> phenix.autobuild \ >> >> write_run_directory_to_file=/someplace/home/someuser/work/someproject/ >> phenix2/AutoBuild_run_1_/TEMP0/INFO_FILE_1 >> >> Reading effective parameters from /someplace/home/someuser/work/ >> someproject/phenix2/AutoBuild_run_1_/TEMP0/PARAMS_1.eff >> >> Sending output to AutoBuild_run_1_/AutoBuild_run_1_1.log >> >> ******************************************************************************** >> >> Failed to carry out AutoBuild_build_cycle: >> >> failure >> >> ******************************************************************************** >> >> ******************************************************************************** >> >> work_pdb_file "AutoBuild_run_1_/edited_pdb.pdb" >> working_directory "/someplace/home/someuser/work/someproject/phenix2" >> worst_percent_res_rebuild 2.0 >> >> --------------------------------------------------- >> Alex Berndt >> MRC-Laboratory of Molecular Biology >> Hills Road >> Cambridge, CB2 0QH >> U.K. >> >> phone: +44 (0)1223 402113 >> --------------------------------------------------- >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

17 years, 4 months

Re: [phenixbb] high average b-factor vs. Wilson B - EXPLANATION

by Sue Roberts

Hello, I'm a little confused about Pavel's response. Perhaps I'm not understanding it correctly. I don't understand why you say this is nothing to worry about. It seems to me that it means that the refinement strategy isn't stable or optimal - the contributions from the overall Baniso and the individual B factors are not being (and prossibly can not be) separated properly - maybe they can't be because the overall anisotropy is so large that it swamps the anisotropic B or perhaps the resolution is not sufficient to refine anisotropic Bs for individual atoms. In these cases shouldn't either (1) the anisotopic B be refined and then fixed rather than be allowed to creep up or (2) anisotropic Bs for individual atoms not be refined? Can this problem be debugged by looking at the anisotropic Bs in coot? If the anisotropic scale is being incorporated improperly into the atomic anisotropic Bs then would all the thermal ellipsoids have almost the same shape and orientation and only differ in magnitude? Sue On Aug 6, 2010, at 9:15 AM, Pavel Afonine wrote: > Hi Geoffrey, > > thanks for sending me the data and model - this helped me to find out what happens in your and other similar repeatedly reported cases. > > Have a quick look at the total model structure factor formula that is used in all phenix.refine, phenix.model_vs_data, phenix.maps and many other similar tools: > > see page 6 here: > > http://www.phenix-online.org/presentations/latest/pavel_refinement_general.… > > and glance through the page 29, PHENIX Newsletter: > > http://www.phenix-online.org/newsletter/CCN_2010_07.pdf > > As you see there is overall anisotropic scale matrix Ucryst (see Acta Cryst. (2005). D61, 850-855 and references therein for deeper level of details). In refinement, the trace of this matrix is subtracted from it and added to individual ADPs and Bsol, making Fmodel invariant under this manipulation. Most of the time, this is a small value, but sometimes it is relatively large. > > Now, let's see what happens in your particular case. > The Wilson B-factor is 27. > If we reset all B-factors to 27 and repeat the refinement until convergence using two scenarios: > > 1) we add the trace of Ucryst to individual ADPs, > 2) we do not add the trace of Ucryst to individual ADPs, > > we will get the following: > > 1) R-work = 0.1728, R-free = 0.2177 > Bcryst (Ucryst reported as B) = (-10.42,-11.48,21.90,-0.00,0.00,0.00); trace/3= 0.00 > ksol= 0.33 Bsol= 54.75 > Average ADP = 43.56 > > 2) R-work = 0.1744, R-free = 0.2171 > Bcryst (Ucryst reported as B) = (4.42,3.35,36.58,0.00,0.00,0.00); trace/3= 14.78 > ksol= 0.32 Bsol= 40.00 > Average ADP = 29.03 > > Clearly, in case "2)" you get almost exact match of Wilson B and Average ADP (27 and 29), while in case "1)" the B-factors are higher. Note, the R-factors in both cases are "identical" (negligibly different given the resolution and the R-factor value). > > So I guess everything is more or less consistent and clear. It depends where and how you keep different contributions to the total ADP, and which values you use to compute mean ADP. > > Answering your very original question "Should I be concerned about this?": the answer is no. But I had a quick look at your maps: and this is what I would spend some more time: you have a lot of positive and negative peaks, some of them are very strong: larger than 6sigma! I guess you are missing some ions, and alternative conformations may need some more attention. This is normal, it just needs some care and time to be spent before your structure is ready to go (to PDB). > > Pavel. > > PS> I'm sending you the results of these two runs off list. > > > On 8/3/10 10:20 PM, Geoffrey Feld wrote: >> Dear PhenixBBers, >> >> I'm working on a 1.45 A structure I solved using MR (phaser) and I'm pretty close to finishing, just plopping in waters and fixing rotamers. Rw = 19.8 Rfree= 22.8. I am a little concerned because my Wilson B is 27.00 while my average B for macromolecule is more like 43, and for solvent is 48. I have enough data to use anisotropic ADP refinement, which was a big help in bringing down the Rfree, but the average B hasn't really moved much. Should I be concerned about this? Should I try adjusting the wxu, or some other parameter? >> >> Thanks! > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1041 E. Lowell St., Tucson, AZ 85721 Phone: 520 621 8171 suer(a)email.arizona.edu http://www.biochem.arizona.edu/xray

15 years, 6 months

Search results for query "look through"