- phenixbb - phenix-online.org

Re: [phenixbb] XN-refinement
by Pavel Afonine 17 Oct '16

17 Oct '16

>> this is good to hear, and this demonstrates the power of using more data. The only issue here, as I mentioned before, is that in joint XN refinement we refine one single model against two data sets, while ideally it should be two models in order to account for genuine unique information that is contained in X-ray and neutron data. This will be addressed at some point. >> > Out of curiosity, could you elaborate on why it would be preferred to refine two separate models? It seems to me, admittedly not having any experience with neutron diffraction, that the ultimate goal is to model the system of the crystal, and given 2 data sets, we would want to create the single model describing the structure in the crystal that best agrees with all the available data. Are the neutron and X-ray data so different that using them for joint refinement is disadvantageous? I think I wrote that already in previous email.. Structures corresponding to two data sets are of course overall similar may be different in local details: - Different X-H(D) distances (see figure 4 here: http://journals.iucr.org/d/issues/2010/11/00/dz5209/index.html) - Different data collection temperatures: -- Different B factors; -- Different visible water structure; -- Different local disorder (that may be captured as distinct conformations at low temperature, but may be blurred at higher temperature); - Different completeness and resolution of one data set may allow features in one model corresponding to this data set that may not be supported by the other data set. For example, you may see a well resolved water with one or two D in neutron map but you may not even see any water at all in X-ray map, or the other way around. - etc etc etc. So it is advantageous to use both X-ray and neutron data sets together but these nuances need to be carefully taken care of which isn't the case in current implementations of joint XN refinement protocols. This makes a good room for future improvements. Pavel

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constrain insertion codes to unit occupancy?
by van den Bedem, Henry 15 Oct '16

15 Oct '16

Hi: I’m refining a site where there’s two compounds, each at partial occupancy. I modeled that using alt codes and insertion codes combined, like this ATOM 6500 CA ACYS B 101B ATOM 6490 CA BXXX B 101A How can I constrain the occupancies so that they sum to unity? I tried several option, but the distinct insertions seem to refine independently. Sorry if a similar question has been posted before, but I could not find a solution searching phenixbb. Thanks! Henry

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XN-refinement
by Johannes Schiebel 14 Oct '16

14 Oct '16

Hi everyone, I am currently working on an X-ray/neutron (XN) joint refinement using phenix.refine. As it should be, H/D coordinates and ADPs at exchangable sites are refined to equal values when using Phenix version 1.10.1-2155 and neutron data only. This is also stated in the paper describing the development of the method (Afonine et al. (2010) Joint X-ray and neutron refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 66, 1153-1163) as the default behavior: "Currently, phenix.refine maintains the H and D atoms at coinciding positions and constrains their ADPs to be equal to each other". However, when switching to XN-refinement using the same Phenix version, H and D atoms refine to different coordinates and ADPs, which should not be the case as it leads to unrealistic artifacts as can be seen from the deposited PDB 3X2P: ATOM 186 H AALA A 13 3.486 -18.200 -14.123 0.38 14.54 H ATOM 187 D BALA A 13 3.488 -18.195 -14.111 0.62 38.07 D In this example, the D-occupancy is likely overestimated, while the H-occupancy is underestimated because the ADPs refine to very different values, which is chemically not reasonable. Hence my question: How can I treat my data in a way that ADPs and coordinates refine to the same values at exchangeable H/D sites also for XN-refinement? Is there a specific keyword I am currently overlooking or do I have to use another Phenix version? I would be really glad to receive your feedback. Thanks in advance! Kind regards, Johannes

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Unknown parameter file format
by Jan van Agthoven 11 Oct '16

11 Oct '16

Hi everyone, I used my refinement parameters in the following format in the latest phenix: custom_par.params And it returned: Sorry: Unknown file format: custom_par.params Anyone knows how to solve this? Thanks, Jan

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Re: [phenixbb] Highly anisotropic data
by Pavel Afonine 07 Oct '16

07 Oct '16

Hi Kostya, phenix.resolution reports effective resolution of data set. It is based on methods described here: J. Appl. Cryst. (2015). 48, 589-597 Acta Cryst. (2013). D69, 1921-1934 As I pointed out before, a single number for highest resolution isn't very informative unless you show data completeness per resolution (in phenix.refine log file it is reported in the beginning of macro-cycles right after bulk-solvent step). Pavel On 10/7/16 00:15, Kogan, Konstantin wrote: > Dear all, > > Thank you for your comments. The maps are not that bad, and actually > from biological point of view we do see everything we want. One of the > questions is how to report the parameters for the structure, as I have > a feeling that the effective resolution is much lower than 2.64Å, > which is the current limit, and the mean B value is twice higher than > estimated Wilson B value. All together it seems that this is the data > I have, but I would like to be sure, that I have got maximum out of it. > > I attach the xtriage log file for more information, if needed. Also I > attached the example of a good map region at 1.6 sigma and a bad map > region at 1.0 sigma. > > I have also tested to refine at 2.8, 2.9, and 3.0, and I haven't seen > much difference in maps quality, but the Rwork/Rfree went down a bit. > > Isn't is seems a bit suspicious 2.64Å resolution, > Rwork/Rfree=0.28/0.31, and mean B value 114? Is there a way to > present/report effective resolution? > > Kostya > > > > > Hi Kostya, > > how complete the data set is? Missing reflections in some resolution > zones between 2.64A and inf may be sufficient to make the effective > resolution lower or much lower than 2.64A which would explain why the > map does not look like what you expect. > > Pavel > > > On 05/10/16 22:53, Randy Read wrote: >> Hi, >> >> As Christian said, the level of anisotropy is not that bad for this >> structure. In terms of what Phenix can do to handle it, first, when >> you solved it by MR, Phaser would have accounted explicitly for the >> anisotropy. In fact, Phaser’s algorithms underlie the anisotropy >> server that produced your plot! Phenix.refine will also refine the >> overall anisotropy parameters. >> >> When you have really severe anisotropy, the current algorithms may >> not account well enough for the differing accuracy of reflections in >> the weak directions. So it can sometimes be helpful to do >> anisotropic pruning of the data in the way that the anisotropy server >> implements it. But this is something to do with some caution, and I >> think you should only press on with it if the maps allow you to see >> things you couldn’t see clearly before. >> >> Best wishes, >> >> Randy Read >> >> ----- >> Randy J. Read >> Department of Haematology, University of Cambridge >> Cambridge Institute for Medical Research Tel: +44 1223 336500 >> Wellcome Trust/MRC Building Fax: +44 1223 336827 >> Hills Road E-mail: rjr27(a)cam.ac.uk >> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk >> >>> On 5 Oct 2016, at 20:32, Christian Roth <christianroth034(a)gmail.com> >>> wrote: >>> >>> Hi Kostya, >>> >>> I have seen worse data than that, which are ususally treated quite >>> well within phenix using standard parameters. With a resolution of >>> about 2.7 Ang. I wouldn't expect to see waters and also just well >>> ordered side chains, whereas more flexible ones just give some >>> "bumps" pointing away from the main chain density. Though without a >>> picture or something else it is difficult to say if your maps are >>> really unusually bad. >>> >>> Cheers >>> >>> Christian >>> >>> Am 05.10.2016 um 07:47 schrieb Kogan, Konstantin: >>>> Dear all, >>>> >>>> I have highly anisotropic data. I was able to solve the structure >>>> by MR, and refine it with phenix.refine to Rwork/Rfree=0.28/0.31 >>>> with Resolution cutoff 2.64Å and mean B values 114, which is pretty >>>> high for such resolution. Though the overall structure makes sense, >>>> the maps are quite featureless, no water molecules, and side-chains >>>> refinement is a problem. I have tested how the data is anisotropic >>>> with Diffraction Anisotropy Server (see attached image), which >>>> shows clearly, that we don't really have data to 2.64Å in all >>>> directions. Though, there are other servers/programs that can deal >>>> specifically with anisotropic data e.g. STARANISO anisotropy server >>>> and then refine with BUSTER, I would like to know if it's possible >>>> still to use Phenix with some more advance parameters to actually >>>> address the issue of anisotropy and to get maximum out of the data. >>>> The space group is P61 2 2, cell parameters are 73, 73, 453, 90, >>>> 90, 120 and I have high multiplicity data, but no NCS. >>>> >>>> Thanks in advance for any input, >>>> >>>> Kostya >>>> -- >>>> Konstantin (Kostya) Kogan >>>> Postdoctoral researcher >>>> Pekka Lappalainen's Lab >>>> Institute of Biotechnology >>>> University of Helsinki >>>> Helsinki, Finland >>>> Mobile: +358-(0)45-8994342 >>>> >>>> >>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> >>>> phenixbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>> >>>> Unsubscribe: >>>> phenixbb-leave(a)phenix-online.org >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> Unsubscribe: phenixbb-leave(a)phenix-online.org

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Option to select array from mtz in phenix.real_space_refine?
by Oliver Clarke 06 Oct '16

06 Oct '16

Hi, I find phenix.real_space refine very effective for initial refinement of a model against a density modified map after molecular replacement (with morphing and reference restraints etc enabled). However, when I do this it seems like if there is more than one array of map coefficients in the file there is no way to select which columns to use, unlike for phenix.refine - would it be possible to add such an option? Currently I just use cad in ccp4 to make a file with the desired columns, but it would be a smoother process if the desired column labels could be specified directly at run time. Cheers Oli

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Highly anisotropic data
by Kogan, Konstantin 06 Oct '16

06 Oct '16

Dear all, I have highly anisotropic data. I was able to solve the structure by MR, and refine it with phenix.refine to Rwork/Rfree=0.28/0.31 with Resolution cutoff 2.64Å and mean B values 114, which is pretty high for such resolution. Though the overall structure makes sense, the maps are quite featureless, no water molecules, and side-chains refinement is a problem. I have tested how the data is anisotropic with Diffraction Anisotropy Server <https://services.mbi.ucla.edu/anisoscale/> (see attached image), which shows clearly, that we don't really have data to 2.64Å in all directions. Though, there are other servers/programs that can deal specifically with anisotropic data e.g. STARANISO anisotropy server <http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi> and then refine with BUSTER, I would like to know if it's possible still to use Phenix with some more advance parameters to actually address the issue of anisotropy and to get maximum out of the data. The space group is P61 2 2, cell parameters are 73, 73, 453, 90, 90, 120 and I have high multiplicity data, but no NCS. Thanks in advance for any input, Kostya -- Konstantin (Kostya) Kogan Postdoctoral researcher Pekka Lappalainen's Lab Institute of Biotechnology University of Helsinki Helsinki, Finland Mobile: +358-(0)45-8994342

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Planarity restraint ignored when dist_esd equal to 0
by Keitaro Yamashita 28 Sep '16

28 Sep '16

Dear PHENIX developers, My colleague noticed that planarity restraint of a ligand was ignored when a cif file in CCP4 monomer library was given to phenix.refine. The cif file was $CLIBD_MON/3/3PG.cif. This was because phenix (mmtbx) ignores planarity restraint when dist_esd is 0. In the line 2055 of mmtbx/monomer_library/pdb_interpretation.py (phenix-1.10.1), plane_atom is not added to the list when (plane_atom.dist_esd in [None, 0]) is True. _chem_comp_plane_atom.dist_esd in 3PG.cif (ccp4-7.0) is all zero except the first atom in the plane definition. As far as I checked, there is no cif file where dist_esd of the first atom of plane is zero. At least, it would be helpful if phenix shows warning in this case. Best regards, Keitaro

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How to define Fobs labels for phenix.refine in command line mode
by Karthikeyan Subramanian 27 Sep '16

27 Sep '16

Dear All, Is it possible to define the Fobs (or) Iobs labels for phenix.refine in command line mode? Thanks Karthikeyan S. IMTECH, Chandigarh India

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Rotamers of unnatural halogenated amino acids
by ancacarl 26 Sep '16

26 Sep '16

Hi, I'm working on the refinement of a protein mutated with an unnatural amino acid that contains one bromine atom. This particular amino acid is present as two rotamers. I've managed to introduce and do refinements with these two unnatural, brominated rotamers in Phenix, but the problem is that when shooting the protein with X-rays about 30-40% of the bromine atoms get knocked off. This means that the sum of the occupancies for the bromine atoms of the rotamers needs to be less than 1.00. However, the total occupancy of all the other rotamer atom pairs must be 1.00. Is there a way in Phenix to refine rotamers of brominated, unnatural amino acids, and at the same time have the total occupancy less than 1.00 for the Br atoms only? Any advice how to solve this is welcome.

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