- phenixbb - phenix-online.org

Occupancy issue
by Simon Kolstoe 15 May '12

15 May '12

Hi phenixbb, I'm wanting to refine the occupancy for just a few Cadmium atoms in a structure but not refine any other occupancies. I've used the following command however the occupancies haven't refined: phenix.refine refinement_006.def occupancies.individual="chain X and element CD2" and the cadmiums are in the pdb file as: ATOM 8740 CD+2 CD2 X 1 -81.043 91.612 65.218 1.00 11.63 X CD2+ ATOM 8741 CD+2 CD2 X 2 -78.111 92.072 62.948 1.00 11.15 X CD2+ ATOM 8742 CD+2 CD2 X 3 -85.283 28.170 80.931 1.00 12.01 X CD2+ Thanks, Simon

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Refinement error with Se labeled DNA cif seting
by Lauren 15 May '12

15 May '12

Dear all, I have a protein complex with 10mer DNA with one adenine labeled with Se-CH3 at C2'. I gave the se labeled pdb structure to the Elbow or ReadySet, the program gave me the cif as shown below. When I tried to refine the structure, phenix.refine ends with a Error message: Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unexpected atoms: {'AMS,OP1': 1, 'AMS,OP2': 1} Classifications: {'DNA': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM 2 OP1 AMS A 1 .*.A O " "HETATM 3 OP2 AMS A 1 .*.A O " Any advice on how to modified the cif or pdb files? Thanks so much in advance. CIF files: AMS P P P . 10.3639 38.8090 53.6083 AMS OP1 O OH1 . 9.8621 39.4308 52.7650 AMS OP2 O O . 9.6270 38.9790 55.3430 AMS O5' O O2 . 11.5188 37.6926 53.7178 AMS C5' C CH2 . 12.2621 37.6244 54.8065 AMS C4' C CR15 . 13.5128 36.9044 54.7141 AMS O4' O O . 14.2653 37.1385 55.8584 AMS C3' C CR15 . 13.2442 35.4155 54.6698 AMS O3' O OH1 . 14.1003 34.8289 53.7923 AMS C2' C CR15 . 13.5010 34.9324 55.9516 AMS SE2' SE SE . 11.8697 34.2402 56.7089 AMS C1' C CR15 . 13.9654 36.1199 56.7679 AMS CA' C CH3 . 11.5566 32.3937 56.0481 AMS N9 N NR5 . 15.1526 35.8937 57.6065 AMS C8 C CR15 . 16.4077 35.6661 57.1789 AMS N7 N N . 17.1943 35.5119 58.2703 AMS C5 C CR56 . 16.4320 35.6429 59.3887 AMS C4 C CR56 . 15.1196 35.8884 58.9705 AMS N1 N N . 15.6651 35.7647 61.7193 AMS C2 C CR16 . 14.4119 35.9994 61.2874 AMS N3 N N . 14.1134 36.0657 59.9478 AMS C6 C CR6 . 16.7122 35.5796 60.8007 AMS N6 N NH2 . 18.1110 35.3174 61.2840 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd AMS P OP1 single 1.162 0.02 AMS P OP2 double 1.892 0.02 AMS P O5' single 1.610 0.02 AMS O5' C5' single 1.320 0.02 AMS C5' C4' single 1.446 0.02 AMS C4' O4' single 1.389 0.02 AMS C4' C3' single 1.514 0.02 AMS O4' C1' single 1.398 0.02 AMS C3' O3' single 1.359 0.02 AMS C3' C2' single 1.394 0.02 AMS C2' SE2' single 1.927 0.02 AMS C2' C1' single 1.514 0.02 AMS SE2' CA' single 1.986 0.02 AMS C1' N9 single 1.471 0.02 AMS N9 C8 aromatic 1.345 0.02 AMS N9 C4 aromatic 1.364 0.02 AMS C8 N7 aromatic 1.354 0.02 AMS N7 C5 aromatic 1.360 0.02 AMS C5 C4 aromatic 1.399 0.02 AMS C5 C6 aromatic 1.441 0.02 AMS C4 N3 aromatic 1.414 0.02 AMS N1 C2 aromatic 1.346 0.02 AMS N1 C6 aromatic 1.405 0.02 AMS C2 N3 aromatic 1.374 0.02 AMS C6 N6 single 1.503 0.02 Best Regards Lauren

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refinement of peptide with non-standard aminocids
by Vitali Stanevich 15 May '12

15 May '12

Hi, I am trying to refine protein structure with MCLR ligand - this is cyclic hepta-peptide which has some non-standard amino acids. Sequence is DAL-LEU-ACB-ARG-1ZN-FGA-DAM. It's exactly the same compound as chain G at 3dw8 PDB entry. I could successfully import amino acids in coot through "get monomer" option, renumber and combine in one chain. Problem is that whenever I use phenix.refine it returns all residues nonbonded. Corresponding carboxyl and amino groups are in close proximity to make a bond. I tried to write LINKR record in .pdb - with no success: ... LINKR 1ZN G 5 FGA G 6 trans LINKR FGA G 6 DAM G 7 trans ... Is there a way to create peptide bonds in this inhibitor chain? I'm using phenix Version: 1.7.3. Thanks in advance, Vitali

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discrepancy in MolProbity statistics
by Michael Thompson 15 May '12

15 May '12

Hello All, I recently ran into a discrepancy between the MolProbity statistics reported by phenix.refine and the MolProbity statistics reported by the actual MolProbity webserver. I was hoping someone could comment on this and let me know if this is a warning sign that something is amiss. The structure (resolution=2.0A) seems to be correct and well refined, based on R-factors (0.1591/0.1774) and geometry reports from the various validation tools. Remark 3, which was written out to the pdb file by phenix.refine, contains the following: REMARK 3 MOLPROBITY STATISTICS. REMARK 3 ALL-ATOM CLASHSCORE : 4.14 REMARK 3 RAMACHANDRAN PLOT: REMARK 3 OUTLIERS : 0.00 % REMARK 3 ALLOWED : 2.32 % REMARK 3 FAVORED : 97.68 % REMARK 3 ROTAMER OUTLIERS : 1.83 % REMARK 3 CBETA DEVIATIONS : 0 Remark 40, which was created by and downloaded from the MolProbity web server, contains slightly different statistics: REMARK 40 MOLPROBITY OUTPUT SCORES: REMARK 40 ALL-ATOM CLASHSCORE : 0.83 REMARK 40 BAD ROTAMERS : 1.6% 8/510 (TARGET 0-1%) REMARK 40 RAMACHANDRAN OUTLIERS : 0.0% 0/657 (TARGET 0.2%) REMARK 40 RAMACHANDRAN FAVORED : 97.7% 642/657 (TARGET 98.0%) I am mainly concerned about the values of the ALL-ATOM CLASHSCORE, as they are significantly different according to the two calculations. Thanks in advance for any information/answers! Mike -- 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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phenix.model
by r n 14 May '12

14 May '12

Hi I did get different values in phenix.model_vs_data, after the refinement gave me R and Rfree as 24 and 29% and phenix.model_vs_data gave me R_compute and Rfree-compute as 22 and 26%. Thought that both R-compute and refinement values should be more or less same? any suggestions R

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CASP 10: Call for targets to assess the state of the art in protein structure modeling
by Torsten Schwede 11 May '12

11 May '12

*CASP 10: Call for targets to assess the state of the art in protein structure modeling* As many of you know, CASP (Critical Assessment of Structure prediction) has been assessing the state of the art in modeling protein structure from sequence since 1994, running a community experiment once every two years. In these experiments, information on soon to be solved structures is collected from the experimental community, and the sequence data are passed to the structure modeling community so that blind predictions of structure and can collected and assessed (1). Over that period CASP has seen enormous progress in the quality of modeled structures (2), but many problems remain. CASP is only possible because of the generous participation of the experimental community in providing the modeling targets (3). We recently appealed for your help in providing novel fold and membrane protein targets for the ongoing CASP ROLL process. That is very successful, with 57 prediction teams participating and 26 targets already released, thanks to all of you who have contributed. The prediction season for the next full biannual experiment, CASP 10, begins May 1, and so we are now asking for your help again, this time in reaching our goal of releasing at least varied 100 targets in a the three-month period. We need all sorts of targets, spanning the categories below: 1. (More than ever) novel folds and membrane protein targets -- even with the extended collection season provided by CASP ROLL, there will be still a shortage. There are some interesting methods developments for ab initio modeling, and it is important to be able to decisively evaluate their effectiveness. 2. A diversity of comparative modeling targets. Cases where the there is fairly high sequence identity (30-50%) between the target structure and an available template are valuable for testing the degree to which model accuracy can approach that of experiment, particularly in functionally critical regions. Cases with lower sequence identity to template, right down to undetectable, are valuable for testing the ability of the methods to detect remote homologs, to overcome challenging alignment difficulties, to make use of multiple templates, and to build regions of the structure not obviously available from a template. 3. Targets containing significant amounts of disordered structure, so as to test the ability of methods to identify these regions. Disorder identified by absence of density in crystallography is current the main source and very useful, but its important to have cases where the nature of the disorder has been established by other means, such as NMR. 4. Some targets will also be used to test methods of structure refinement. In these cases, the best model received for a target will be released to the refinement community, who will subsequently submit new models. This too is an area where there have been some exciting developments in the last year, so we are hoping for significant progress. Refinement targets are selected based on the nature of the errors in the initial models. Because of the extended process, these targets need to be available for longer before release of the experimental structure. For those of you who have not provided targets to CASP before, the procedure is simple. There are three ways to submit targets: (1) Go the target submission web page and fill in the easy form; (2) When you submit your co-ordinates to the PDB, tick the 'CASP HOLD' box, automatically setting up a target entry; (3) Send an email the prediction center with details. If you have queries, there is a very experienced prediction center staff to deal with them. The key thing is timing: We need a window of at least four weeks between receiving information about a target and the release of your experimental structure. A longer window -- up to eight weeks - is often useful, for example so that a target can be used to test refinement methods, but is not essential (note that using the PDB target submission route automatically selects eight weeks). We don't need your experimental structure in advance of its release by the PDB, provided that will happen by the end of August. Please consult the target submission page for more details: http://www.predictioncenter.org/casp10/targets_submission.cgi There are already over 200 prediction teams signed for CASP 10, and so any targets provided will receive plenty of attention. If you have a suitable target now, we are ready to receive it. If new targets come up before July 17, we would also love to have them. (After July 17, we will continue with CASP ROLL for novel folds and membrane proteins). So please get in touch whenever a suitable opportunity arises, and help improve modeling methods. Thanks, CASP organizing committee John Moult, IBBR, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, SIB & Biozentrum University of Basel, Switzerland Anna Tramontano, University of Rome, Italy Get in touch: casp(a)predictioncenter.org More information: http://www.predictioncenter.org/casp10/index.cgi CASP Roll targets so far: http://www.predictioncenter.org/casprol/targetlist.cgi Submit a target: http://www.predictioncenter.org/casp10/targets_submission.cgi 1. Critical assessment of methods of protein structure prediction (CASP)--round IX. <http://www.ncbi.nlm.nih.gov/pubmed/21997831> Moult J, Fidelis K, Kryshtafovych A, Tramontano A. Proteins. 2011;79 Suppl 10:1-5. doi: 10.1002/prot.23200. Epub 2011 Oct 14. 2. CASP9 results compared to those of previous CASP experiments. <http://www.ncbi.nlm.nih.gov/pubmed/21997643> Kryshtafovych A, Fidelis K, Moult J. Proteins. 2011;79 Suppl 10:196-207. doi: 10.1002/prot.23182. Epub 2011 Oct 14 3.Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. <http://www.ncbi.nlm.nih.gov/pubmed/22020785> Kryshtafovych A et al. Proteins 2011;79 Suppl 10:6-20. doi: 10.1002/prot.23196. Epub 2011 Oct 21.

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Fwd: Re: anisotropic induced noise amplification
by Pavel Afonine 11 May '12

11 May '12

Hi, I realized Randy's reply did not go to the mailing list, so I'm forwarding it now. Pavel -------- Original Message -------- Subject: Re: [phenixbb] anisotropic induced noise amplification Date: Mon, 7 May 2012 09:49:57 +0100 From: Randy Read <rjr27(a)cam.ac.uk> To: Pavel Afonine <pafonine(a)lbl.gov> CC: developers(a)phenix-online.org <developers(a)phenix-online.org>, Peter Zwart <PHZwart(a)lbl.gov> In the absence of an answer from Peter (who implemented this and therefore ought to know best), I'm pretty sure that the idea is to measure how much difference there is in the amount of signal in the data that have received the biggest anisotropy corrections, compared to the ones that have received the smallest anisotropy corrections. If there's very little signal in the data that have been scaled up the most, then the noise is being amplified (nearly-random amplitudes have gone from being relatively small to the same size on average as the well-measured amplitudes). But what the Z-scores mean is not at all clear from that output, and I'm not aware that Peter has written anything describing this. This amplified noise is what I suspect is creating problems in phenix.refine refinement with highly anisotropic data, because if the experimental sigmas are ignored then the program doesn't know (after anisotropic scaling) which amplitudes of a comparable size contain signal and which are essentially noise. Anisotropic truncation gets rid of it, which would explain why refinement works better with anisotropically-truncated data. Randy On 6 May 2012, at 20:21, Pavel Afonine wrote: > Hi, > > did anyone address this post? I'm interested to know the answer > myself: I have absolutely no idea what is this. > > Pavel > > -------- Original Message -------- > Subject: [phenixbb] anisotropic induced noise amplification > Date: Wed, 2 May 2012 16:06:55 -0500 > From: James Thompson <Thompson.James(a)mayo.edu> > Reply-To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > To: phenixbb(a)phenix-online.org > > > > 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* > > <Attached Message Part.txt> ------ 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 <mailto:[email protected]> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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lastest phenix.refine reproducible problem
by 周文昌 09 May '12

09 May '12

Dear all, I've been learning phenix refinement on a MAD dataset which is already deposited in PDB. There are something I can not get through. Basically I had two steps refinement: 1->phenix.refine data.mtz model.pdb xray_data.high_resolution=3 fix_rotamers=true strategy=individual+adp+individual_sites+tls 2->phenix.refine data.mtz model-refined.pdb xray_data.high_resolution=3 fix_rotamers=false strategy=none main.number_of_macro_cycles=1 model-refined.pdb is actually from the 1st step, so in principle the R/R-free values should be the same for 1 and 2. However in my case, I had 0.2506/0.2996 for the 1st step but 0.2503/0.2998 for the second. I compared the resulting pdb and mtz files from the two steps. PDB model were exactly the same but there were little difference in the mtz file. Why there is difference in mtz file and would it be the reason for the difference of R factors? I use the latest version of phenix, phenix-dev-1009. thanks, Wenchang

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Installation on a POWER 7 system
by Rajagopalan, Senapathy 09 May '12

09 May '12

Hi Everyone, I was wondering if its possible to install PHENIX on a POWER 7 system. The cluster for which we have access runs on a power 7 system and at least my initial try to install the FC3 version failed. 'uname –rm' gives me '2.6.32-220.13.1.el6.ppc64 ppc64'. If only re-compilation is required, I would appreciate if you can point me in the right direction. Thanks Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list seven years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at methodisthealth.com. Follow us at twitter.com/MethodistHosp and www.facebook.com/MethodistHospital. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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NCS, TLS and anisotropic b-factors
by Morten Groftehauge 08 May '12

08 May '12

Hi Phenixbb, Just one more stupid question: On the phenix website it says under *current limitations of phenix.refine*"Atoms with anisotropic ADP in NCS groups". I take this to mean that phenix.refine doesn't handle the combination of TLS and NCS well, is this correct? So what is the correct way of handling TLS and NCS? Do one run where individual, isotropic ADP+xyz and NCS are refined and then another where individual, isotropic ADP+xyz and TLS are refined? Or one run where individual, isotropic ADP+xyz and NCS are refined and then another where individual, isotropic ADP and TLS are refined? Or does the issues go away if you only use torsional NCS? Or adjusting the B-factor weight of NCS selections? Should B-factor weight then be set up or down? Okay, that was more than one question but at least they're all on the same topic. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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