May 2012 - phenixbb - phenix-online.org

phenix.refine crashes
by Jianghai Zhu 08 May '12

08 May '12

Hi, I am using phenix.refine dev-1051. When I was trying flip_peptide, it crashes with the following error messages. Validate: |--------START--------| |--------FINAL--------| residue map_cc 2mFo-DFc mFo-DFc map_cc 2mFo-DFc mFo-DFc Traceback (most recent call last): File "/home/jzhu/phenix/phenix-dev-1051/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/jzhu/phenix/phenix-dev-1051/phenix/phenix/refinement/command_line.py", line 146, in run call_back_handler=call_back_handler) File "/home/jzhu/phenix/phenix-dev-1051/phenix/phenix/refinement/driver.py", line 1499, in run ncs_manager = self.ncs_manager) File "/home/jzhu/phenix/phenix-dev-1051/phenix/phenix/refinement/strategies.py", line 928, in refinement_machine params = params.flip_peptides) File "/home/jzhu/phenix/phenix-dev-1051/cctbx_project/mmtbx/refinement/flip_peptides.py", line 445, in run log=log) File "/home/jzhu/phenix/phenix-dev-1051/cctbx_project/mmtbx/refinement/fit_rotamers.py", line 749, in validate_changes sites_cart=sites_cart) File "/home/jzhu/phenix/phenix-dev-1051/cctbx_project/mmtbx/refinement/flip_peptides.py", line 152, in __call__ return (self.rama_lookup.evaluate_sites(res_type,i_seqs,sites_cart)<0.002) File "/home/jzhu/phenix/phenix-dev-1051/cctbx_project/mmtbx/rotamer/ramachandran_eval.py", line 76, in evaluate_sites "isoleucine or valine"]) AssertionError -- Jianghai

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Re: [phenixbb] phenixbb Digest, Vol 78, Issue 9
by CPMAS Chen 08 May '12

08 May '12

Thank you all. Actually, as Pavel said there is a easy way to do so, I changed the cif file of the ligand, where I had restraints on the dihedral modified. Message: 3 > Date: Sat, 05 May 2012 13:48:06 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] how to define a molecule in two rigid_body > Message-ID: <4FA59206.7090207(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Charles, > > I think you are trying to achieve two goals, "keep conformation you > like" and "make sure it fits given density", while one of the two > contradicts to the other. That is either the density you are trying to > fit in your molecule or your expectations about the geometry of the > molecule (or both) are not quite right. > > I think this is how much one can tell given the information you provided. > > I don't think you need to do that sophisticated rigid-body kind of > refinement that you described in your original post. The solution must > be easier. May be if you send me the model and data and tell which part > of the model you think is in trouble then probably I could help more. > > Pavel > > On 5/5/12 10:22 AM, Nathaniel Echols wrote: > > On Sat, May 5, 2012 at 6:39 AM, CPMAS Chen<cpmasmit(a)gmail.com> wrote: > >> I am almost at final stage. but the refinement always shows error > density at > >> the single bond connecting the two rings. I have tried manually change > the > >> orientation of these two rings, but there are two concerns that I > thought > >> why I did not get the perfect fitting. > >> 1. I might not choose the perfect the orientation of these rings, and > these > >> give me a non-perfect fitting, and high b-factor. > >> 2. since phenix always tries to change the conformation a little bit to > fit > >> the density, so this also might cause some errors, or not the > conformation I > >> like. > >> > >> Then, my sense is that, if I can somehow define the two parts of the > >> molecule as two rigid bodies, then phenix only can has free rotation of > >> these two rings, and the fitting might come out good. > > You can define custom planarity restraints for the rings - there isn't > > good documentation for this, but here is what to do: > > > > 1. If you're using the command line, look here in the .eff file: > > > > refinement { > > geometry_restraints { > > edits { > > planarity { > > atom_selection = resseq 1001 and (name C1 or name C2 or name > > C3 or name C4 or name C5 or name C6) > > sigma = 0.1 > > } > > } > > } > > } > > > > (Other parameters omitted for clarify, of course. I'm not sure what > > an appropriate sigma would be - you'll probably have to experiment.) > > > > 2. If you're using the GUI, make sure you have the latest nightly > > build, and on the middle configuration tab, click "Custom geometry > > restraints", which will open a window that includes a tab for creating > > planarity restraints. > > > > Technically, the two planes won't actually be "rigid bodies" (i.e. > > "constrained"), but if you make the planarity restraint sufficiently > > tight there will be very little deviation from ideality. (Just don't > > make it too tight, or you'll confuse the minimizer.) > > > > -Nat > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > > > ------------------------------ > > -- *************************************************** CPMAS Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Difficult dataset and refinement--P422? I422?Twinning?
by Zhou, Tongqing (NIH/VRC) [E] 07 May '12

07 May '12

Dear All, I have collected several dataset for an antibody:antigen complex. It apparently indexed to P4 space group with large cell dimensions of 191.7000/191.7000/311.0540. When I processed as P1 and ran Pointless, it suggested P422 as space group. P4212 gives the best MR solution with 6 mol/ASU (18 chains total ). However, ridigbody and subsequent refinement with TLS could not reduce the r and r-free which stayed at ~48%. Tried to go P4, P222...(12 mol/ASU) with twinning, but the refinement failed due to insufficient computer memory (12 GB), it was also impossible to refine in P1 due to the same reason. But for some data sets, HKL2000 also gave I4 space group with c axis reduced to 1/3 of that of P4. With the I4 data (~2.7 A resolution), I422 was the best MR space group (1 mol/ASU), the refinement went down to r=29% and r-free=34%, but won't go down further. Please advise if it's possible to use the data Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

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how to define a molecule in two rigid_body
by CPMAS Chen 05 May '12

05 May '12

Thanks, Ralf. I am almost at final stage. but the refinement always shows error density at the single bond connecting the two rings. I have tried manually change the orientation of these two rings, but there are two concerns that I thought why I did not get the perfect fitting. 1. I might not choose the perfect the orientation of these rings, and these give me a non-perfect fitting, and high b-factor. 2. since phenix always tries to change the conformation a little bit to fit the density, so this also might cause some errors, or not the conformation I like. Then, my sense is that, if I can somehow define the two parts of the molecule as two rigid bodies, then phenix only can has free rotation of these two rings, and the fitting might come out good. Charles %%%%%%%%%%%%%%%%%%%%% University of Pittsburgh School of Medicine Department of Aneshesiology %%%%%%%%%%%%%%%%%%%%%

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how to define a molecule in two rigid_body
by CPMAS Chen 05 May '12

05 May '12

Dear Colleagues, First, I would say sorry to bother your guys at Friday evening. :) I have a molecule which has two rings connected by a single bond. I would like this two rings freely rotate around the single bond, but keep each ring conformation fixed (as there are sidechains connected to each ring). Could you help me do this rigid_body definition, or suggest a better idea to do so in phenix? Regards and Thanks! Charles Chen. %%%%%%%%%%%%%%%%%%%%% University of Pittsburgh School of Medicine Department of Aneshesiology %%%%%%%%%%%%%%%%%%%%%

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geometry weight optimization with mlhl target
by Mooers, Blaine H.M. (HSC) 04 May '12

04 May '12

Dear Phenixbb, How does one optimize geometry when using the mlhl target in refinement with Henderson-Lattman coefficients in the input reflection file? The wxc_scale keyword is not recognized when I used the mlhl target, but it is recognized when I use the ml target by setting main.use_experimental_phases=false. Blaine Blaine Mooers Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: blaine-mooers(a)ouhsc.edu<mailto:[email protected]> webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/…

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secondary structure restraints helices/helixes proline
by Morten Groftehauge 04 May '12

04 May '12

Hi guys, How does phenix.refine handle prolines in helices? When I look in high resolution structures it seems that the carbonyl of the residue four positions before the proline (also in the helix) should be more perpendicular than parallel to the helix. This makes sense since there isn't any nitrogen for it to hydrogen bond to. But when I refine my structure it seems as if phenix.refine is trying to push the carbonyl into parallel position. Am I imagining things? It's not the best data and this is a troublesome region. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Re: [phenixbb] Geometry Restraints - Anisotropic truncation
by Terwilliger, Thomas C 03 May '12

03 May '12

Hi Kendall, Yes, I think you could use this kind of approach to make overall decisions of any kind, including those you suggest. I would not use Rsleep for anything at all, other than calculating a final number. I would use a fixed Rfree set (which could be a subset of the total free set or the whole set) for all such decision making. If a lot of such decisions are made with Rfree...then yes it would be good to have an Rsleep to make sure that everything is ok. All the best, Tom T ________________________________ From: Kendall Nettles [knettles(a)scripps.edu] Sent: Thursday, May 03, 2012 9:05 AM To: Terwilliger, Thomas C; PHENIX user mailing list Subject: Fwd: [phenixbb] Geometry Restraints - Anisotropic truncation Hi Tom, Do you think something like this could be used during refinement to identify the "best" resolution limits? If you have an Rsleep set would Rfree be sufficient for this? I imagine collecting data with a ring of noise and then let the optimal resolution be determined during refinement. My understanding of this is that the modern refinement algorithms can handle some noise in the reflections, but maybe this could be a way to optimize how much signal is needed to contribute in a positive fashion? Kendall

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Re: [phenixbb] Geometry Restraints - Anisotropic truncation
by Leonid Sazanov 03 May '12

03 May '12

Hi, so will we see now the possibility to apply anisotropic resolution limits truncation in Phenix? Despite the fact that a lot of people use UCLA server, there is still no possibility to do this in any major crystallographic software, AFAIK. Phaser does the scaling, but no truncation, and noise sitting in those regions where there is no signal, is a real culprit. Large SIGFs there do not resolve the problem completely. Thanks. >>>>>> Message: 4 Date: Wed, 25 Apr 2012 09:05:57 -0400 From: Mario Sanches <mariosan(a)gmail.com> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: [phenixbb] Geometry Restraints - UPDATE .......... It turns out that the reason to my nightmares was a highly anisotropic dataset. When I tried to fix geometry related problems in coot, phenix.refine was twisting the geometry back again, probably because it was trying to fit a lot of noise due to the anisotropy. Everything was getting worst, geometry, clashscore, and Ramachandran. Pavel finally corrected it by using this server: http://services.mbi.ucla.edu/anisoscale/ ............ -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Secondary Structure Definitions
by Antony Oliver 03 May '12

03 May '12

Dear all, Is there a phenix jiffy to assign (and write!) secondary structure definitions to a pdb file? I'm currently using MacPyMOL to put together some figures, and I can see that some of the secondary structure elements in the cartoon representation aren't being drawn correctly. Being slightly old-school, I used to use DSSP and the little program dssp2pdb to extract the information and put it into the PDB header. Is there a simpler / easier way to do this? (NB: I'm aware that CCP4MG copes better with SS assignment, but I prefer to use PyMOL in this instance). With thanks, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk<mailto:[email protected]> tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512

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Fwd: Geometry Restraints - Anisotropic truncation
by Kendall Nettles 03 May '12

03 May '12

Hi Tom, Do you think something like this could be used during refinement to identify the "best" resolution limits? If you have an Rsleep set would Rfree be sufficient for this? I imagine collecting data with a ring of noise and then let the optimal resolution be determined during refinement. My understanding of this is that the modern refinement algorithms can handle some noise in the reflections, but maybe this could be a way to optimize how much signal is needed to contribute in a positive fashion? Kendall From: "Terwilliger, Thomas C" <terwilliger(a)lanl.gov<mailto:[email protected]>> Date: May 3, 2012 10:23:29 AM EDT To: PHENIX user mailing list <phenixbb(a)phenix-online.org<mailto:[email protected]>> Subject: Re: [phenixbb] Geometry Restraints - Anisotropic truncation Reply-To: PHENIX user mailing list <phenixbb(a)phenix-online.org<mailto:[email protected]>> Hi Kendall, This could work. You could define a fixed set of test reflections, and never touch these, and never include them in refinement, and always use this fixed set to calculate a free R. Then you could do whatever you want, throw away some work reflections, etc, refine, and evaluate how things are working with the fixed free R set. All the best, Tom T ________________________________________ From: phenixbb-bounces(a)phenix-online.org<mailto:[email protected]> [phenixbb-bounces(a)phenix-online.org<mailto:[email protected]>] on behalf of Kendall Nettles [knettles(a)scripps.edu<mailto:[email protected]>] Sent: Thursday, May 03, 2012 7:05 AM To: PHENIX user mailing list Subject: Re: [phenixbb] Geometry Restraints - Anisotropic truncation Hi Pavel, Could you use a similar approach to figuring out where to cut your data in general? Could you compare the effects of throwing out reflections in different bins, based on I/sigma, for example, and use this to determine what is truly noise? I might predict that as you throw out "noise" reflections you will see a larger drop in Rfree than from throwing out "signal" reflections, which should converge as you approach the "true" resolution. While we don't use I/sigma exclusively, we do to tend towards cutting most of our data sets at the same i/sigma, around 1.5. It would be great if there was a more scientific approach. Best, Kendall On May 3, 2012, at 7:45 AM, Pavel Afonine wrote: Hi Kendall, removing same amount of data randomly gives Rwork/Rfree ~ 30/35%. Pavel On 5/3/12 4:13 AM, Kendall Nettles wrote: Hi Pavel, What happens if you throw out that many reflections that have signal? Can you take out a random set of the same size? Best, Kendall On May 3, 2012, at 2:41 AM, "Pavel Afonine"<pafonine(a)lbl.gov<mailto:[email protected]>> wrote: Hi Kendall, I just did this quick test: calculated R-factors using original and anisotropy-corrected Mike Sawaya's data (*) Original: r_work : 0.3026 r_free : 0.3591 number of reflections: 26944 Truncated: r_work : 0.2640 r_free : 0.3178 number of reflections: 18176 The difference in R-factors is not too surprising given how many reflections was removed (about 33%). Pavel (*) Note, the data available in PDB is anisotropy corrected. The original data set was kindly provided to me by the author. On 5/2/12 5:25 AM, Kendall Nettles wrote: I didnt think the structure was publishable with Rfree of 33% because I was expecting the reviewers to complain. We have tested a number of data sets on the UCLA server and it usually doesn't make much difference. I wouldn't expect truncation alone to change Rfree by 5%, and it usually doesn't. The two times I have seen dramatic impacts on the maps ( and Rfree ), the highly anisotrophic sets showed strong waves of difference density as well, which was fixed by throwing out the noise. We have moved to using loose data cutoffs for most structures, but I do think anisotropic truncation can be helpful in rare cases. Kendall On May 1, 2012, at 3:07 PM, "Dale Tronrud"<det102(a)uoxray.uoregon.edu<mailto:[email protected]>> wrote: While philosophically I see no difference between a spherical resolution cutoff and an elliptical one, a drop in the free R can't be the justification for the switch. A model cannot be made more "publishable" simply by discarding data. We have a whole bunch of empirical guides for judging the quality of this and that in our field. We determine the resolution limit of a data set (and imposing a "limit" is another empirical choice made) based on Rmrg, or Rmes, or Rpim getting too big or I/sigI getting too small and there is no agreement on how "too big/small" is too "too big/small". We then have other empirical guides for judging the quality of the models we produce (e.g. Rwork, Rfree, rmsds of various sorts). Most people seem to recognize that the these criteria need to be applied differently for different resolutions. A lower resolution model is allowed a higher Rfree, for example. Isn't is also true that a model refined to data with a cutoff of I/sigI of 1 would be expected to have a free R higher than a model refined to data with a cutoff of 2? Surely we cannot say that the decrease in free R that results from changing the cutoff criteria from 1 to 2 reflects an improved model. It is the same model after all. Sometimes this shifting application of empirical criteria enhances the adoption of new technology. Certainly the TLS parametrization of atomic motion has been widely accepted because it results in lower working and free Rs. I've seen it knock 3 to 5 percent off, and while that certainly means that the model fits the data better, I'm not sure that the quality of the hydrogen bond distances, van der Waals distances, or maps are any better. The latter details are what I really look for in a model. On the other hand, there has been good evidence through the years that there is useful information in the data beyond an I/sigI of 2 or an Rmeas> 100% but getting people to use this data has been a hard slog. The reason for this reluctance is that the R values of the resulting models are higher. Of course they are higher! That does not mean the models are of poorer quality, only that data with lower signal/noise has been used that was discarded in the models you used to develop your "gut feeling" for the meaning of R. When you change your criteria for selecting data you have to discard your old notions about the acceptable values of empirical quality measures. You either have to normalize your measure, as Phil Jeffrey recommends, by ensuring that you calculate your R's with the same reflections, or by making objective measures of map quality. Dale Tronrud P.S. It is entirely possible that refining a model to a very optimistic resolution cutoff and calculating the map to a lower resolution might be better than throwing out the data altogether. On 5/1/2012 10:34 AM, Kendall Nettles wrote: I have seen dramatic improvements in maps and behavior during refinement following use of the UCLA anisotropy server in two different cases. For one of them the Rfree went from 33% to 28%. I don't think it would have been publishable otherwise. Kendall On May 1, 2012, at 11:10 AM, Bryan Lepore wrote: On Mon, Apr 30, 2012 at 4:22 AM, Phil Evans<pre(a)mrc-lmb.cam.ac.uk<mailto:[email protected]>> wrote: Are anisotropic cutoff desirable? is there a peer-reviewed publication - perhaps from Acta Crystallographica - which describes precisely why scaling or refinement programs are inadequate to ameliorate the problem of anisotropy, and argues why the method applied in Strong, et. al. 2006 satisfies this need? -Bryan _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb

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How to include restraints when refining DNA?
by Xun Lu 03 May '12

03 May '12

Dear all, I am refining a protein-DNA complex structure at 2.9A resolution. The R/Rfree is 0.2181/0.2501, which is pretty good, but I can tell that the DNA is not well refined. Some sugar puckers are not right. The distances between some base-paired bases are kind of short (~2.5A). I've tried including a reference model for the DNA, or including a cif file, and I've also tried to turn on the secondary_structure_restraints.... nothing worked. I must have not done it in a correct way. But how to do it? And how to deal with sugar puckers? In refmac, I can set the distances between bases during the refinement, so there must be a way to do it in phenix as well? Any advice is welcome. Thanks! Xun -- Department of Molecular and Structural Biochemistry North Carolina State University

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anisotropic induced noise amplification
by James Thompson 02 May '12

02 May '12

Anyone willing to summarize Xtriage's algorithm that determines whether "anisotropic induced noise amplification" is present in diffraction data? What is this noise amplification? Is it anisotropic correction factors that over-fit the data thereby inducing noise? Many thanks, Jim T ---------------- Anisotropy analyses ---------------- Anisotropy ( [MaxAnisoB-MinAnisoB]/[MaxAnisoB] ) : 3.596e-01 Anisotropic ratio p-value : 0.000e+00 The p-value is a measure of the severity of anisotropy as observed in the PDB. The p-value of 0.000e+00 indicates that roughly 100.0 % of datasets available in the PDB have an anisotropy equal to or worse than this dataset. For the resolution shell spanning between 2.36 - 2.20 Angstrom, the mean I/sigI is equal to 3.37. 42.2 % of these intensities have an I/sigI > 3. When sorting these intensities by their anisotropic correction factor and analysing the I/sigI behavior for this ordered list, we can gauge the presence of 'anisotropy induced noise amplification' in reciprocal space. The quarter of Intensities *least* affected by the anisotropy correction show <I/sigI> : 3.82e+00 Fraction of I/sigI > 3 : 5.01e-01 ( Z = 3.59 ) The quarter of Intensities *most* affected by the anisotropy correction show <I/sigI> : 2.02e+00 Fraction of I/sigI > 3 : 1.84e-01 ( Z = 10.78 ) The combined Z-score of 11.36 indicates that there probably is significant systematic noise amplification that could possibly lead to artefacts in the maps or difficulties in refinement

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Re: [phenixbb] Scaling of diffraction data
by jens j birktoft 02 May '12

02 May '12

Hi Everybody, Is there a protocol for re-scaling several sets of diffraction data against a common reference set, either native or based on a Fcalc set computed from a common input model. The are from a number of derivatives, are all isomorphus, and are anomalous data . We want to compare the relative peak heights in Fo-Fc and Anom. difference maps Cheers Jens +++++++++++++++++++++++++++++++++++++++++++++++++++ Jens J. Birktoft e-mail: birktoft @ nyu.edu <jens.knold(a)gmail.com> ; Phone: 212-749-5057 +++++++++++++++++++++++++++++++++++++++++++++++++++

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Xtriage problem
by Abhinav Kumar 02 May '12

02 May '12

Hi, When I try to do R vs R analysis for calculated data using xtriage, it has a problem accepting calc labels. source /home/sw/rhel5/x86_64/phenix/phenix-1.7.3-928/phenix_env phenix.xtriage_1.7.3-928 junk.mtz calc_labels=FC ==> Sorry: No matching array: scaling.input.xray_data.calc_labels=FC Howevere, it works fine with an earlier version: source /home/sw/rhel5/x86_64/phenix/phenix-1.6.4-486/phenix_env phenix.xtriage_1.6.4-486 junk.mtz calc_labels=FC Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 -------- Original Message -------- Subject: RE: SP16569N-180314 Date: Tue, 1 May 2012 15:09:00 -0700 From: Miller, Mitchell D. <mmiller(a)slac.stanford.edu> To: Kumar, Abhinav <abhinavk(a)slac.stanford.edu> Hmm, it seems like it may be a bug introduced into phenix. (or else they changed they syntax and did not update the documentation) Can you report it? I get it to do the RvR analysis for calculated data if I use source /home/sw/rhel5/x86_64/phenix/phenix-1.6.4-486/phenix_env phenix.xtriage_1.6.4-486 junk.mtz calc_labels=FC but if I use source /home/sw/rhel5/x86_64/phenix/phenix-1.7.1-743/phenix_env phenix.xtriage_1.7.1-743 junk.mtz calc_labels=FC or source /home/sw/rhel5/x86_64/phenix/phenix-1.7.3-928/phenix_env phenix.xtriage_1.7.3-928 junk.mtz calc_labels=FC then I get the error Sorry: No matching array: scaling.input.xray_data.calc_labels=FC Thanks, Mitch P.S. the results I got were: R vs R statistic: R_abs_twin =<|I1-I2|>/<|I1+I2|> Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 R_abs_twin observed data : 0.451 R_abs_twin calculated data : 0.502 R_sq_twin =<(I1-I2)^2>/<(I1+I2)^2> R_sq_twin observed data : 0.279 R_sq_twin calculated data : 0.335 The analyses of the Patterson function reveals a significant off-origin peak that is 44.82 % of the origin peak, indicating pseudo translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo translational symmetry is equal to the 1.4447e-04. See the relevant section of the logfile for more details. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. Even though no twinning is suspected, it might be worthwhile carrying out a refinement using a dedicated twin target anyway, as twinned structures with low twin fractions are difficult to distinguish from non-twinned structures. -----Original Message----- From: Kumar, Abhinav Sent: Tuesday, May 01, 2012 1:30 PM To: Miller, Mitchell D. Subject: Re: SP16569N-180314 I am having trouble inputting Calc labels to xtriage: My mtz file has the following columns: FreeR_flag FP SIGFP FC PHIC FC_ALL PHIC_ALL FWT PHWT DELFWT PHDELWT FOM PHCOMB I tried "FC,PHIC" and "FC" for calc labels but xtriage does not like it. It writes: No matching array: scaling.input.xray_data.calc_labels=FC Possible choices: /mnt/exdsstaff/abhinavk/Refine/SP16569N-180314/RESULTS/current.mtz:FP,SIGFP /mnt/exdsstaff/abhinavk/Refine/SP16569N-180314/RESULTS/current.mtz:FOM /mnt/exdsstaff/abhinavk/Refine/SP16569N-180314/RESULTS/current.mtz:PHCOMB Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 On 05/01/2012 12:51 PM, Miller, Mitchell D. wrote: Also, you could try running xtriage with FC's from the untwined refinement to look at the R vs R stats for Fc vs Fobs.

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Re: [phenixbb] Geometry Restraints - Anisotropic truncation
by Frank von Delft 02 May '12

02 May '12

Hi Pavel > we discussed this with Randy the other day.. A couple of copy-pasts from > that discussion: > > In general, given highly anisotropic data set: > > 1) maps calculated using all (unmodified) data by phenix.refine, > phenix.maps and similar tools are better than maps calculated using > anisotropy truncated data. So, yes, for the purpose of map calculation > there is no need to do anything: Phenix map calculation tools deal with > anisotropy very well. How did you define "better"? If there are a lot of reflections without signal, that makes them essentially missing, so by including them, you're effectively filling in for those reflections with only DFc. If anisotropy is very strong (i.e. many missing reflections), does that not introduce very significant model bias? The maps would look cleaner, though. (I haven't tested myself, btw; I'm genuinely wondering.) > 2) phenix.refine refinement may fail if one uses original anisotropic > data set. This is probably because the ML target does not use > experimental sigmas (and anisotropy correction by UCLA server is nothing > but Miller index dependent removing the data by sigma criterion - yeah, > that old well criticized practice of throwing away the data that you > worked hard to measure!). May be using sigmas in ML calculation could > solve the problem but that has to be proved. If there are large swathes of reciprocal space without signal - I don't see why shouldn't that be excluded? Tossing out individual reflections is of course silly, but what's wrong with trimming down the edges of the elipsoid? Cheers phx

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Inputting DNA for Phenix MR and/or Autobuild
by Charles Allerston 02 May '12

02 May '12

Dear all, I can't find much in the way of documentation for this. Can someone point me to some please? I basically want to know the correct format for entering DNA into the search for MR and inputting into Autobuild. If I have a double stranded DNA do I enter it as >DNA1 AATT:AATT >DNA1 AATT TTAA etc. ? cheers, charlie Dr. Charles Allerston Genome Integrity & Repair Structural Genomics Consortium Nuffield Department of Medicine Old Road Campus University of Oxford OX3 7DQ http://www.thesgc.org/scientists/groups/oxford/genome-integrity-and-repair

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Call for submissions to June 2012 Computational Crystallography Newsletter (CCN)
by Nigel Moriarty 01 May '12

01 May '12

Calling for articles and short communications of interest to structural biologists. The deadline for publication in the June 2012 issue is 29 May, 2012. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and the template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Estimation of ligand binding affinity by occupancy refinement
by Zoran Stefanic 01 May '12

01 May '12

Dear all, I have a question about sensitivity of occupancy refinement in phenix. I have a series of datasets done at our home instrument of relatively modest resolutions from 2.8 to 3 A. These are performed on crystals soaked in progressively higher ligand concentrations. We are trying to see to which of the several active sites the ligand binds first so we went from low to high ligand concentrations. We wanted to estimate the amount of ligand bound by refining the occupancies of the ligand. We expect one active site to bind more strongly than the other two active sites. This was indeed what we observed but when we refine the occupancies of the ligands in weaker binding sites starting at 0.2 occupancies they rise to 0.5-0.6 although some atoms are totally out of density and some are in. B factors are reasonable, i.e. don't go wild. My question would be: how reliable is this estimation of ligand binding by occupancy refinement? Why doesn't the occupancy of ligands stay low if afterwards the density fit of the ligand looks rather unconvincing? Thank you in advance Zoran -- Dr. Zoran Stefanic Division of Physical Chemistry Rudjer Boskovic Institute Bijenicka 54 P.O. Box 180 Zagreb Croatia Phone: 00 385 1 457 1203 Fax: 00 385 1 468 0245

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