- phenixbb - phenix-online.org

EG4 not in phenix dictionary?
by Yarrow Madrona 03 Jun '13

03 Jun '13

Hello, I have previously refined EG4 and EG2 (tetra and diethylene glycol) as ligands and these were in the standard phenix library. I was under the impression that phenix shares the library from the CCP4 monomer library which I know should have EG4. Can anyone help me with this. I guess the alternative is to generate a restraints file. -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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MAX IV Life Science Director position
by Derek Logan 03 Jun '13

03 Jun '13

Hi, If anyone fancies becoming Life Science Director at the world's brightest light source, look no further than here: http://www.lunduniversity.lu.se/o.o.i.s?id=24914&Dnr=547454&Type=E /Derek ________________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se<http://www.cmps.lu.se> Centre for Molecular Protein Science www.maxlab.lu.se/node/307<http://www.maxlab.lu.se/node/307> Lund University, Box 124, 221 00 Lund, Sweden

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Re: [phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"
by Michael Thompson 01 Jun '13

01 Jun '13

As another follow up to this point, I have had a recent example where Xtriage reported that my intensity statistics indicated twinning (<|L|>=0.399 and <L^2>=0.227, alpha=0.4). After having refined the structure with the suggested twin law, and making composite omit maps along the way (using autobuild with no twin law), I ran model vs. data at the end of refinement and noticed that it reported R/Rfree that were about 10% higher than the R/Rfree from refinement, similar to what the original post described. I checked the model vs. data logfile and found that the L-test routine used by model vs. data was failing, so the subsequent analysis was carried out as if there was no twinning. So in my case, the crystal was twinned, but model vs. data was not able to perform the L-test so it was outputting incorrect R-factors. The error message at the top of the model vs. data log file is: Twin analysis failed: Python argument types in l_test.__init__(l_test, miller_index, double, space_group, bool, float, float, float, int) did not match C++ signature: __init__(_object*, scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor> miller_indices, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> intensity, cctbx::sgtbx::space_group space_group, bool anomalous_flag, long parity_h, long parity_k, long parity_l, unsigned long max_delta_h) Twin analysis failed: Python argument types in l_test.__init__(l_test, miller_index, double, space_group, bool, float, float, float, int) did not match C++ signature: __init__(_object*, scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor> miller_indices, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> intensity, cctbx::sgtbx::space_group space_group, bool anomalous_flag, long parity_h, long parity_k, long parity_l, unsigned long max_delta_h) Perhaps there are some other users who are seeing this behavior because the L-test fails within model vs. data. Mike ----- Original Message ----- From: "Nathaniel Echols" <nechols(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Wednesday, May 29, 2013 5:18:57 PM GMT -08:00 US/Canada Pacific Subject: Re: [phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1" On Wed, May 29, 2013 at 4:13 PM, Sam Stampfer <Samuel.Stampfer(a)tufts.edu> wrote: > When I refined my model in phenix, I used the twin law h,-h-k,-l. I read in > the documentation that twinning can account for some of this discrepancy, > but that the program is supposed to take twinning into account if it will > lower the calculated R-work by more than 2%, which it doesn't seem to have > done (or there is some other problem with my data). Okay, the problem is that your data don't actually appear to be twinned. The automatic method used by phenix.model_vs_data (which is used internally for Table 1 and the validation GUI) only tries possible twin laws if the results of the "L test" show a suspicious distribution of intensities. Your data look fine, so it doesn't bother trying the twin laws. That the R-factors are lower when you refine with a twin law isn't necessarily indicative of the data actually being twinned - Garib Murshudov has looked into this in detail but I confess to being ignorant of the math (but I can probably dig up his paper on the subject if anyone is interested). However, I'm pretty sure the data are actually in a higher-symmetry space group. Will send details and new files off-list (probably tomorrow at this rate). I should probably change some of the programs and/or documentation to make it more clear what is being done internally, since it took me a bit of digging to realize what was going on. In general, though, always be very careful before running twinned refinement! I have seen several users do this by mistake when they really had higher symmetry. The maps will also be more model-biased when using twinned refinement, so it's good to avoid doing this unless absolutely necessary. -Nat _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- 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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Re: [phenixbb] refinement of partly occupied water molecules?
by krimmer＠staff.uni-marburg.de 31 May '13

31 May '13

Dear Nathaniel, dear Pavel, thank you for your fast answers! > currently phenix.refine can add automatically only fully occupied > waters (I am not sure it will ever use atomic model for partially > occupied waters). If necessary, add partially occupied waters > yourself manually. Make sure they have properly set altlocs > (alternative location identifiers): non blank (say A and B). Is it current praxis to let phenix.refine freely refine the occupancy of water molecules (adding partially occupied water molecules in coot and don’t fix the occupancy in phenix)? If I do so, these water molecules are refined by phenix.refine with occupancies between 0.4-0.8. My resolution range was 1.1 – 1.4 Å. > The nightly builds have an option in phenix.refine to place ions > automatically based on a variety of criteria (still being tuned). > However, what you describe doesn't sound like any ion coordination > motif that I've read about. Could you please send us a picture that > shows the density in context? Some of the other readers with more > experience in "blobology" may recognize it. [if our list server > complains about the size of the message, just ignore it, I'll approve > it for posting] Attached you will find the image of the blob. I think it’s easily visible that the density blob is in the middle of the five-ring and that there is also a (smaller) blob in the middle of the six-ring. The water which occupies the blob was not yet refined with phenix, I just put it there to measure the distances to the carbon atoms. Best regards, Stefan

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gap between Wilson B and average B
by fn1＠rice.edu 30 May '13

30 May '13

Dear all, I have a structure at about 3.5 A, which has a wilson B of about 109 and has an average B factor from model is only 49 (I did not use TLS). I read from the previous posts that wilson B is sometimes smaller than average B, but in my case it is reversed. I look at the distribution of model B factors, they are in the range of 8 to 132. Is there any problem with the refinement of this structure? Thanks in advance for all advice! Regards, Fengyun

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refinement of partly occupied water molecules?
by krimmer＠staff.uni-marburg.de 30 May '13

30 May '13

Dear all, I have a question concerning the refinement of partly occupied water molecules: in some of my macromolecular crystal structures with resolutions between 1.1 - 1.4 Å, mainly in the second solvation shell round positive Fo-Fc electron density blobs are detectable which show after assignment of a water molecule to these blob and subsequent refinement with Phenix refine a good-looking calculated 2Fo-Fc electron density (round shape, the 2Fo-Fc map appears at a contour level of σ = 1.0 - 1.4), but there also occurs a small negative Fo-Fc electron density detectable inside the 2Fo-Fc density blob. The negative Fo-Fc electron density disappears if the occupancy of the water molecule is refined by Phenix or manually set lower than 100% occupancy. Therefore, I think these positions are partly occupied by water molecules, but I am not sure how I should handle it/how it is generally handled. I would be thankful for any advice and/or literature about this topic. My second question is concerning a density blob in perfect coordination distance to an indolyl group (perfectly located in the middle of the five-ring, with 3.4 Å distance to every of the five carbon atoms of the five-ring). What‘s the best way to find out which ion possibly occupies this position? I tried Na+ and Ca2+, but after refinement big negative Fo-Fc blobs appear in both cases (maybe the ion at this position is only partly occupied?). There is no anomalous signal detectable at this position (data collection wavelength was 0.91841 nm). After the refinement of a water molecule at this position, a positive Fo-Fc election density is still there. Thank you for your help! Stefan

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R-merge
by Mengbin Chen 29 May '13

29 May '13

Dear Phenix Users, I have R-merge values equal 0.000 from highest resolution shell (which corresponds to values larger than 1.000) in a data set processed by HKL2000, with redundancies higher than 10 (I know this may help in increasing R-merge). I am not sure if this is going to be a problem of Table 1 for the reviewers. Could you kindly drop me your suggestions? Thank you in advance, Mengbin Chen -- Mengbin Chen Department of Chemistry University of Pennsylvania

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phenix.refine using anomalous concepts for neutron data?
by Derek Logan 29 May '13

29 May '13

Hi, I'm doing a joint X-ray neutron refinement in Phenix and have run into some behaviour that puzzles me. I had not been paying any attention to the use or non-use of anomalous signal in the neutron dataset, as This is what I get if I let phenix.refine itself decide whether or not to use anomalous data: ================================= Neutron data ================================ F-obs: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM Miller array info: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM Observation type: xray.reconstructed_amplitude Type of data: double, size=16672 Type of sigmas: double, size=16672 Number of Miller indices: 16672 Anomalous flag: True Unit cell: (removed) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 1258 Resolution range: 29.22 1.89826 Completeness in resolution range: 0.785008 Completeness with d_max=infinity: 0.78486 Bijvoet pairs: 6832 Lone Bijvoet mates: 1750 Anomalous signal: 0.0876 Number of F-obs in resolution range: 16672 Number of F-obs<0 (these reflections will be rejected): 0 Number of F-obs=0 (these reflections will be used in refinement): 0 Refinement resolution range: d_max = 29.2200 d_min = 1.8983 and this is what I get if I forcibly switch off use of anomalous data in the phenix.refine GUI: ================================= Neutron data ================================ F-obs: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM Miller array info: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM Observation type: xray.reconstructed_amplitude Type of data: double, size=16672 Type of sigmas: double, size=16672 Number of Miller indices: 16672 Anomalous flag: True Unit cell: (removed) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 1258 Resolution range: 29.22 1.89826 Completeness in resolution range: 0.785008 Completeness with d_max=infinity: 0.78486 Bijvoet pairs: 6832 Lone Bijvoet mates: 1750 Anomalous signal: 0.0876 force_anomalous_flag_to_be_equal_to=False Reducing data to non-anomalous array. R-linear = sum(abs(data - mean(data))) / sum(abs(data)) R-square = sum((data - mean(data))**2) / sum(data**2) In these sums single measurements are excluded. Redundancy Mean Mean Min Max Mean R-linear R-square unused: - 29.2234 bin 1: 29.2234 - 4.0863 1 2 1.699 0.0240 0.0011 bin 2: 4.0863 - 3.2448 1 2 1.793 0.0302 0.0022 bin 3: 3.2448 - 2.8350 1 2 1.800 0.0417 0.0041 bin 4: 2.8350 - 2.5760 1 2 1.764 0.0486 0.0054 bin 5: 2.5760 - 2.3914 1 2 1.745 0.0505 0.0051 bin 6: 2.3914 - 2.2505 1 2 1.717 0.0513 0.0051 bin 7: 2.2505 - 2.1378 1 2 1.658 0.0533 0.0056 bin 8: 2.1378 - 2.0448 1 2 1.614 0.0611 0.0074 bin 9: 2.0448 - 1.9661 1 2 1.575 0.0634 0.0075 bin 10: 1.9661 - 1.8983 1 2 1.485 0.0736 0.0097 unused: 1.8983 - Fobs statistics after all cutoffs applied: Miller array info: None Observation type: xray.amplitude Type of data: double, size=9840 Type of sigmas: double, size=9840 Number of Miller indices: 9840 Anomalous flag: False Unit cell: (removed) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 1258 Resolution range: 29.22 1.89826 Completeness in resolution range: 0.855801 Completeness with d_max=infinity: 0.855503 What's going on here? If I let phenix.refine decide automatically, it looks like it's reading in F+ and F- separately and regarding them as independent in the refinement. If I force "no anomalous" it merges them. However I can't work out whether in either case it has actually read FOBS instead of the Friedel mates. According to the SCALA manual the I+ and I- columns will always be written out even if the keyword ANOMALOUS OFF is used, so this is a potential pitfall for many. In addition, phenix.refine seems to identify the neutron data first as xray.reconstructed_amplitude then as xray.amplitude even though the data are explicitly defined as neutron data in the GUI. I can send more information if required! Thanks Derek ________________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se<http://www.cmps.lu.se> Centre for Molecular Protein Science www.maxlab.lu.se/node/307<http://www.maxlab.lu.se/node/307> Lund University, Box 124, 221 00 Lund, Sweden www.saromics.com<http://www.saromics.com>

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Structure Comparison questions
by Heather Condurso 29 May '13

29 May '13

Dear all, I have a few related structures that I would like to compare to make figures for publication but I have a few issues. The biggest issue is that my structures are large (12- 422aa chains) and any attempt at simple alignment in pymol results in a crash. I would like to first compare entire structures, but also compare the differences between related chains in the same structure. I want to look at the small differences in the active site density. What is the best way to do this? Is there a simple way to do this or do I need to make separate pdb files for each chain? Can I use the same mtz or should I rename copies? I will try a few things but any advice would be greatly appreciated. Heather condurso(a)bc.edu

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R: problem refining RNA structure at 4Å resolution
by fulvio.saccoccia＠uniroma1.it 29 May '13

29 May '13

Any signs of twinning? Check also the correctness of your space group: probably you could index In a lower symmetry Laue group with a slight increased distorsion index. Fulvio ----Messaggio Originale---- Da: Benoît Masquida Inviato: 29/05/2013, 14:53 A: PHENIX user mailing list Oggetto: [phenixbb] problem refining RNA structure at 4Å resolution Dear phenix users, I solved using MR a low resolution RNA structure taking data up to 4.3Å and a model of a structure with slight differences. However, when I try to refine, Rwork decreases quickly (start 47, final 32 but Rfree remains high (start 48, final 44). The data are pretty good up to 4.0 with I/sigma above 1. The map doesn't point clearly to wrong regions of the model. What can I try to improve the maps and build the correct model? Thanks in advance. Benoit _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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problem refining RNA structure at 4Å resolution
by Benoît Masquida 29 May '13

29 May '13

Dear phenix users, I solved using MR a low resolution RNA structure taking data up to 4.3Å and a model of a structure with slight differences. However, when I try to refine, Rwork decreases quickly (start 47, final 32 but Rfree remains high (start 48, final 44). The data are pretty good up to 4.0 with I/sigma above 1. The map doesn't point clearly to wrong regions of the model. What can I try to improve the maps and build the correct model? Thanks in advance. Benoit

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Re: [phenixbb] paired refinement in phenix gui
by Kay Diederichs 28 May '13

28 May '13

On Mon, May 27, 2013 at 15:08:26 -0700, Nat Echols wrote: >> >It would be nice if you could confirm if my settings are ok, or if there are >> >still some settings in the background which I overlooked, because we see >> >small changes in R and Rfree. > Changes relative to what? It is not expected that feeding the output > PDB file back to phenix.refine (or another program) will exactly > reproduce the R-factors from the previous round of refinement, because > the precision of the atomic parameters is limited by PDB format. > (Using mmCIF instead would be more reliable, but we don't think a > change in R-factor of 0.0004 is worth worrying about anyway.) > >> >I added the model refined at higher resolution (e.g. 1.5A) and the mtz file >> >cut at CC (e.g.1.5A) in the ?Input data? tab, and set High resolution cutoff >> >in ?X-ray data and experimental phases? box to (e.g. 1.8A) >> >In the refinement setting strategy tab I uncheck everything and set Number >> >of cycles = 1. >> >In ?other options? I uncheck everything too. > This sounds correct, but it's much easier to simply run the validation > GUI, because the underlying code (specifically phenix.model_vs_data) > is designed to calculate identical R-factors to what phenix.refine > shows you. From what I've seen, recent phenix.model_vs_data works correctly and reproduces the statistics from phenix.refine within the numerical accuracy that one can expect. > >> >Alternatively adding a file to the input data with > I don't recommend this - using parameter files as input is fine for > large repetitive parameter blocks such as custom geometry restraints, > selections from the TLSMD server, or nucleic acid base pairs, but > anything that attempts to override the controls in the main GUI may > not work. > >> >2. For whatever reason I would like to do that (molprobity) - can I (and how >> >can I do this) add the command line commands also in the gui? > Could you please clarify? > >> >3. In december 2012 there was a discussion about weak data and refinement. I >> >would like to know if there are new data available showing that ?Whether the >> >benefit they describe is considered cosmetic or non-trivial,.....? > Maybe Kay could comment on this... There is not a single answer that fits all situations. When done correctly (e.g. keeping Rfree flags, keeping refinement strategy), in those cases that I looked at, using weak reflections (cutoff at <I/sigma>~0.5 to 1, cc1/2~0.15-0.25) improved the model's Rfree at lower resolution (paired refinement!) by a few percent, compared to cutting the data at I/sigma>2. Just try it and see if the improvement is worth it, according to your own judgement! > >> >4. Additionally could one short comment on what phenix is doing with strong >> >(weak) reflections marked as aliens in XDS. > Assuming that XDS doesn't actually remove these, phenix.refine may or > may not discard them at the outlier filtering stage (which can be > disabled). I don't know how the different methods for flagging > suspect resolutions compare; Kay and/or Pavel would know more about > this. The "Alien" list in CORRECT.LP was only (originally) meant to alert the user to ice reflections, zingers, and cosmic rays (not sure if the latter play a role, but the former certainly do!). If the "Alien" list just shows reflections at very high resolution, in low-<intensity> resolution shells, then this is due to the fact that Wilson statistics does not hold in these shells, and therefore the algorithm for deciding about "Aliens" is no longer valid. If this happens, you should (as identified in analysis together with James Holton) prevent CORRECT from marking "Aliens" as outliers by changing REJECT_ALIEN from 20 (the default) to 100 or so. Otherwise the mean intensity in that resolution shell will drop (due to rejecting the strongest reflections), and that is bad for applying the Wilson&French algorithm. The XDSCONV in the latest XDS package (identifying itself as March-30-2013) has two fixes for dealing with weak data (again, based on an exchange with James Holton). Unfortunately, a small bug (affecting very few datasets) was identified by Graeme Winter (thanks!) in the XDS program of that package, so be prepared to download the XDS package again in a few days. hope that helps, Kay > >> >According to the supplementary of P. Andrew Karplus, Kay Diederichs ?Linking >> >Crystallographic Model and Data Quality? >> >I would like to do >> >anisotropic refinement, with additional options >> >?ordered_solvent.new_solvent=anisotropic >> >adp.individual.anisotropic="not element H" >> >fix_rotamers=True?. > If your resolution really is 1.5?, I wouldn't recommend making waters > anisotropic. There is some difference of opinion whether anisotropic > refinement of protein atoms is acceptable; it's probably good to try > both ways. (It would be interesting to know whether including the > weak high-resolution data allows you to parameterize the model more > aggressively.) > > -Nat > -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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PDB deposition
by Kay Diederichs 27 May '13

27 May '13

Dear Phenix developers, the following questions came up today, during an attempt to answer the questions that the PDB asks at deposition time: a) For Bulk solvent modeling, what should be given as value for K sol and B sol ? My understanding is that the new solvent model does no longer result in these values; the table is Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work <Fobs> <Fmodel> kiso kani kmask 37.014-13.525 85.34 95 4 7.2146 38.755 318.867 0.937 1.000 0.300 13.240-10.663 91.82 91 10 7.1453 40.328 328.027 0.901 1.000 0.309 10.640-8.570 93.27 202 6 7.4011 38.069 318.901 0.905 1.002 0.310 8.548-6.875 95.70 380 21 7.2679 31.166 258.647 0.901 1.000 0.309 6.871-5.523 95.40 731 36 7.1964 29.485 241.669 0.908 1.001 0.302 5.520-4.439 90.49 1347 61 7.3445 39.504 329.514 0.934 1.001 0.281 4.438-3.568 92.52 2610 150 7.3166 41.793 347.063 0.961 1.000 0.280 3.567-2.867 94.10 5191 231 7.2983 33.593 278.704 0.965 1.000 0.024 2.867-2.304 92.97 9835 476 7.3098 23.922 198.755 0.984 1.000 0.000 2.304-1.852 92.81 18869 947 7.3097 18.746 155.751 1.053 1.000 0.000 1.852-1.488 90.33 35341 1797 7.3288 10.914 90.931 1.035 0.999 0.000 1.488-1.196 86.49 64979 3561 7.2975 6.848 56.810 1.028 0.998 0.000 1.196-1.081 53.28 29672 1567 7.1776 5.351 43.737 0.986 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0072 So what can we do here? b) there is the question about Overall Anisotropic values B11; B22; B33; B12; B13; B23.... but the logfile offers overall anisotropic scale matrix: V0: -0.0214,0.0415,-0.0249,0.0006,-0.0515,-0.0161 V1: -0.0055,-0.0022,0.0080,-0.0001,-0.0020,0.0011 So which of these should be given? I've tried to locate the information about these two questions in the documentation, but it seems I missed it! thanks, Kay

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command line molprobity tools
by Engin Özkan 27 May '13

27 May '13

Hi everybody, I want to create a comprehensive, human-readable log file by running validation using molprobity tools within phenix command-line. I do not have structure factors/maps. Apparently, the GUI runs validation through phenix.model_vs_data (according to the .eff file), but in command-line, I cannot get phenix.model_vs_data to run without an mtz/hkl. I guess I could provide it a fake data file, and then set the comprehensive flag to "True"? BTW, the log file produced by the GUI is not comprehensive at all. I could not find a related mmtbx or cctbx function either. Another mentioned tool, phenix.validate, does not even exist in my installation (dev 1361). Thanks, Engin -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 w ph: (650)-498-7111 cell: (650)-862-8563

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Fwd: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB!
by Paul Adams 24 May '13

24 May '13

Begin forwarded message: > From: Gerard DVD Kleywegt <gerard(a)XRAY.BMC.UU.SE> > Subject: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB! > Date: May 24, 2013 11:20:51 AM PDT > To: CCP4BB(a)JISCMAIL.AC.UK > Reply-To: info(a)wwpdb.org > > Dear colleagues, > > I would like to draw your attention to a notification from the wwPDB partners about "Deposition and Release of PDB Entries Containing Large Structures" - see: > > http://www.wwpdb.org/news/news_2013.html#22-May-2013 > > There are major changes afoot in the way large structures are handled in the PDB, as well as in the deposition and annotation procedures and software used by the wwPDB sites. This is of immediate relevance for depositors and users of large structures, but also for software developers and anyone who routinely processes the entire PDB archive or its weekly releases (bioinformatics resources, etc.). From 2014, it will affect essentially everyone who deposits, uses or processes PDB entries. > > If you have any questions about the new deposition system or the procedures for handling large structures or any of the other changes, please contact: info(a)wwpdb.org > > Please pass on this information to anyone likely to be affected by the upcoming changes. Thanks! > > > On behalf of the Worldwide Protein Data Bank, > > --Gerard Kleywegt > > --- > Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK > gerard(a)ebi.ac.uk ..................... pdbe.org > Secretary: Pauline Haslam pdbe_admin(a)ebi.ac.uk -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Invitation to Participate in a NSF-funded workshop/conference
by Sibo Jiang 24 May '13

24 May '13

Invitation to Participate in a NSF-funded workshop/conference Dear Colleagues in Structural Biology, Recently we have received a NSF grant helping to build the community networks and find solutions for the challenging problems. We have also discussed with the program officer of US National Science Foundation on planning for a research conference/workshop series proposal to US NSF. This conference/workshop series will particularly focus on the technical issues and practical challenges in structural biology of nucleic acids, protein-nucleic acid complexes and small molecule-nucleic acid complexes. These challenges include crystallization, derivatization, phasing and high-resolution structure determination. You are invited to participate in this conference/workshop series. If you are interested in our invitation, please reply this email or send your email to huang(a)gsu.edu<mailto:[email protected]>. In your email, please let us know your name, research interests (up to five key words), affiliation and phone number. The details will be announced later. Colleagues in academia are encouraged to forward this email to your friends and colleagues in industry. Colleagues in industry are particularly welcome. Sincerely, The Planning Committee of the NSF-funded Conference/Workshop

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FW: need suggestion
by afshan490＠yahoo.com 24 May '13

24 May '13

<br/><br/><br/>Sent from Yahoo! Mail for iPhone

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From Dmitri Svergun and Matthias Wilmanns: 11th International Conference: Biology and Synchrotron Radiation (BSR)
by Terwilliger, Thomas C 24 May '13

24 May '13

11th International Conference: Biology and Synchrotron Radiation (BSR) 8-11 September 2013, EMBL Hamburg, Germany Abstract submission deadline is approaching – 1st June 2013! Join us in Hamburg, Germany for BSR 2013! Scientists at all possible career levels are invited to this meeting. Check out our preliminary programme to learn more! http://www.bsr2013.org/BSR13-01/programme/index.html Young researchers are highly welcome to apply for a travel grant from the International Union of Crystallography when registering. http://www.bsr2013.org/BSR13-01/info/index.html Present your work! Selected talks and poster sessions provide great opportunities for participants to present their work. Unique networking opportunities are also available to meet colleagues, friends and future collaboration partners from all over the world. Discover the city of Hamburg! BSR 2013 includes a social programme with boat trips and day and night excursions. Accompanying persons will enjoy special rates! http://www.bsr2013.org/BSR13-01/attractions/index.html A tour of DESY’s most impressive research infrastructures - including PETRA, FLASH and the future X-FEL – is included in the registration fee. http://www.bsr2013.org/BSR13-01/desy/index.html Dates at a glance: · Registration and abstract submission: 1 June 2013 · Registration without abstract: 1 August 2013 Take a look at the updated BSR webpage (www.bsr2013.org<http://www.bsr2013.org>) for more information and to register. CONTACT Diah.Yulianti(a)embl.de<mailto:[email protected]> Alternatively, contact us on the event facebook page https://www.facebook.com/events/332259356868854/

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Call for Proposals: IMAGINE, a New Neutron Crystallography Diffractometer
by Meilleur, Flora 23 May '13

23 May '13

IMAGINE, Neutron Crystallography Diffractometer High Flux Isotope Reactor (HFIR), Oak Ridge National Laboratory Call for proposals for experiments anticipated to run from August through December 2013 You are invited to apply for beam time on the neutron quasi-Laue diffractometer IMAGINE, at the High Flux Isotope Reactor. Proposal will be accepted via the web-based proposal system until NOON Wednesday, July 31, 2013. This call is for experiments anticipated to run from August through December 2013. Please see the attached flyer for additional information. For technical information about the capabilities of IMAGINE go to neutrons.ornl.gov/imagine/<http://neutrons.ornl.gov/imagine/> or contact Flora Meilleur, meilleurf(a)ornl.gov, or Andrey Kovalevsky, kovalevskyay(a)ornl.gov. Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University IMAGINE lead scientist, Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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conflicting bond_simple restraints
by Jianxun Qi 23 May '13

23 May '13

Hi, I had a phosphoserine (SEP) in my structure that is attached in this message. The data_link file for SEP already exists in the mon_lib (data_link_SEPC-N) and the corresponding cif_link I used is as follow: refinement.pdb_interpretation { apply_cif_link { data_link = "SEPC-N" residue_selection_1 = "chain C and resname PHE and resid 3" residue_selection_2 = "chain C and resname SEP and resid 4" } apply_cif_link { data_link = "SEPC-N" residue_selection_1 = "chain C and resname SEP and resid 4" residue_selection_2 = "chain C and resname ARG and resid 5" } } When I run the phenix.refine (my version is phenix-1.8-1069), it said conflicting bond_simple restraints: Sorry: Conflicting bond_simple restraints: 1. definition from: residues: PHE + SEP 2. definition from: residues: PHE + SEP atoms: "ATOM 3121 C PHE C 3 .*. C " "ATOM 3192 N SEP C 4 .*. N " Has anyone ever experienced this case before? Any hints are welcome. Regards Jianxun Qi May 22,2013

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Ca occupancy in multiple soaked structures
by Daniel Slade 22 May '13

22 May '13

Hi Everyone, I have a complex case of data analysis I would love some opinions on. I have a group of structures of a protein that binds 6 calciums, and we want to know the order/concentration at which they fill. The crystals were soaked with calcium from 0-10 mM and all are 1.6-2.1 A in resolution. I determine the order of the calcium binding, and now I am working on the percent occupancy at each concentration. To do this, I have removed the calciums, and then performed simulated annealing for each structure from 2.1-30A resolution to 'normalize' them. I then look at the omit map and scroll out to find the peak sigma intensity of where the calciums should be. The curves fit very well for each calcium, and the numbers correspond well with other solution studies we have. My thought is that I need to normalize this in another way, so I thought choosing a water molecule that is present in all of the structures and removing it, then performing simulated annealing would be a good idea to normalize the peak intensity for each calcium soak concentration, since this water molecule shouldn't change occupancy. Is this the proper way to do this, or can you guys suggest a better way to go about this. I also looked at B factor and e/A3, but that isn't as consistent as peak sigma. Thanks in advance. Dan Daniel J. Slade, Ph.D. Research Associate Thompson Lab The Scripps Research Institute 130 Scripps Way Jupiter, FL 33458 (561) 228-3213

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43rd Mid-Atlantic Macromolecular Crystallography Meeting -- reminder
by Charles Pemble 22 May '13

22 May '13

*43**rd** Mid-Atlantic Macromolecular Crystallography Meeting* *May 30 – June 1, 2013* *Duke University* *Durham, NC* This is a reminder for the 43rd Mid-Atlantic Macromolecular Crystallography Meeting, which will be held next week, May 30-June 01 at Duke University in Durham, North Carolina. Registration and details can be found at http://www.mid-atlantic.org. We encourage you to submit your abstracts for a poster presentation as the deadline is fast approaching! *DEADLINES (updated):* Abstract submission for poster - Next Monday, May 27th *No deadline for registration With best wishes on behalf of the primary Organizing Committee, Charlie Pemble _____________________________ Charles W. Pemble IV, Ph.D. Duke University Medical Center 308 Research Drive LSRC, A06 Durham, NC 27708 charles.pemble(a)duke.edu We thank our current sponsors for their generous contributions: Rigaku Americas Corporation, Agilent Technologies Inc., GlaxoSmithKline, Art Robbins, Bruker, HKL Research Inc., Molecular Dimensions, Hampton Research, Labcyte, GenScript, Genentech, Emerald BioSystems, TTP LabTech, Oxford Cryosystems, PhD Posters, Duke University School of Medicine, Duke Human Vaccine Institute, and Avanti Polar Lipids Inc.

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Workshop - The Future of Microfocus Protein Crystallography - 24-25 September, 2013, Lund, Sweden
by Marjolein Thunnissen 22 May '13

22 May '13

Dear all, I would like to announce a workshop on "The Future of Microfocus Protein Crystallography" which will take place at the MAX IV User meeting on the 24th and the 25th of September, 2013, in Lund, Sweden. Recent developments within protein crystallography methods in combination with the possibilities offered by the new upcoming synchrotron sources such as the MAX IV 3 GeV storage ring make possible exciting new ways of carrying out research within structural biology. Small microfocus beamlines with a very high flux and increased coherence will make new types of experimentation possible. The scientific possibilities will be highlighted through a series of talks by experts showing the impact of the new type of X-ray sources and microfocus beamlines on research within structural biology. The new generation of microfocus beamlines will also set a high demand on instrumentation and suitable software. For example, data collection will potentially be very fast (in milliseconds) and radiation damage will allow only a limited amount of data to be collected from each sample. New technical solutions for sample handling and presentation, data processing methods and more will be needed for these types of experiments, and these will also be presented and discussed at the workshop. Confirmed speakers include David Stuart, Daniel Wacker, Simone Weynand, Jens Preben Morth, Tove Sjögren, Richard Neutze, Janet Smith, Alke Meentz, Alexei Soares, Thomas White and Clemens Schulze-Briese The workshop is part of a process to obtain an updated proposal for the possible Phase 2b beam line MicroMAX at the upcoming new 3 GeV storage ring of MAX IV in Lund. This workshop should give the user community an opportunity to explore the scientific possibilities of a new generation of microfocus beam lines, but also it will give them the chance to contribute with specific input on their own experimental demands on the beam line. The workshop is part of the MAX IV laboratory user meeting. Registration will be through the user meeting website which will open for registration soon. Further information on this workshop can be found at https://www.maxlab.lu.se/node/1609 and for the MAX IV user meeting at https://www.maxlab.lu.se/um13 . For the organisers, Richard Neutze, Gunter Schneider and Gregers Rom Andersen Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

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depositing pdb files
by Mengbin Chen 21 May '13

21 May '13

Hi Phenix Users, I am going to deposit some pdb files into RCSB, which requires Luzzati plots and a bunch of other things. I don't know how to get these results from Phenix (actually the main problem is luzzati errors, Phenix does not seem to provide them), although SFcheck from CCP4i provides only some of them. I know CNS can do this by model_stats.inp, but that's too much trouble since I have complicated ligands bound. Any suggestions would be appreciated! Thank you in advance, Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

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mr_rosetta: how to continue from recovered mr_protocols.default run
by Christian Becke 21 May '13

21 May '13

Hi, I am trying mr_rosetta on a complex. At the GROUP_OF_ROSETTA_REBUILD stage, my machine ran out of memory and the mr_protocols.default processes were killed. After adding more swap space, I restarted the mr_protocols.default runs (3 parallel jobs, one for each chain) using the scripts RUN_?/WORK_?/run_rebuild.sh, which appear to have finished correctly (i.e., there are 20 pdb files generated for each of the chains). However, I could not figure out how to restart mr_rosetta so that it picks up these models. Any suggestions? Thanks, Christian

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