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problem with a twinned data set
by Pascal EGEA 02 Mar '08

02 Mar '08

Hi All This a question of general Crystallography and use of Phenix to deal with twinned data. I am having difficulties with a data set. We have data (2.6 ang resolution) that can be scaled and reduced in P222 with a Rmerge of 7%, the systematic absences show a screw axis ( it is P22(1)2). However MR in Phaser failed in this orthorhombic settings when searching for 2 molecules of the complex in the AU. If we reduce and scale the data in P2(1) and look at the diffraction pattern in HKLVIEW there is a /mmm symmetry. In the monoclinic P2(1) setting we can find 4 molecules of the complex (by MR in Phaser) and can refine it with Phenix to a Rfac/Rfree of 28%/34%. 2 molecules have good electron density whereas the two other ones have one of their domain very poorly defined in density. This is looking very suspicious to me and I am wondering if this refined structure is partially wrong? Meanwhile I used phenix.triage on the data processed in P222 and I am confused with the output. ##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------## Using data between 10.00 to 3.36 Angstrom. Determining possible twin laws. The following twin laws have been found: ------------------------------------------------------------------------ ------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ------------------------------------------------------------------------ ------- | PM | 4-fold | 2.851 | 0.000 | 0.013 | - l,k,h | ------------------------------------------------------------------------ ------- M: Merohedral twin law PM: Pseudomerohedral twin law 0 merohedral twin operators found 1 pseudo-merohedral twin operators found In total, 1 twin operator were found --------------------------------------------- Analysing possible twin law : -l,k,h --------------------------------------------- Results of the H-test on acentric data: (Only 50.0% of the strongest twin pairs were used) mean |H| : 0.368 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.194 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.132 Estimation of twin fraction via cum. dist. of H: 0.115 Britton analyses Extrapolation performed on 0.14 < alpha < 0.495 Estimated twin fraction: 0.127 Correlation: 0.9955 By comparison if I run the detect_twin routine of CNS it tells me that they are no merohedral twin laws for the point group 222 (using the statistical method of Yeates) ? This is confusing me quite a bit. Assuming that the twinning law suggested by Phenix is correct how should I proceed? I have noticed the section concerning refinement using twinned data in Phenix phenix.refine data.hkl model.pdb twin_law="-k,-h,-l" detwin.map_types.aniso_correct=true but It seems I only have a MR solution in P2(1) but not in P222(1) so how can I refine in P222(1) I will greatly appreciate your input, many thanks. Pascal F. Egea, PhD University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory pascal(a)msg.ucsf.edu

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ligand refinement - elbow
by Christine Gee 01 Mar '08

01 Mar '08

Hi Its taken me a while to get around to it, but I just ran elbow to create a cif file etc for my inhibitor, but the bond lengths are quite different from what I got from the PRODRUG server, and it seems that the pdb file I got out of elbow has a few problems (COOT doesn't join up the aromatic ring for example because the carbons are now too far away on one part of the ring). I was wondering how the bond lengths are selected? It seems it is giving the aromatic carbons a bond length of 1.5, when my previous file (and phenylalanine for example have 1.3). Also, I still am not 100% sure how to add the CONNECT information to make the ligand able to covalently bind to the protein. Regards Christine

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refinement problems
by Christine Gee 29 Feb '08

29 Feb '08

Hi This is a more general crystallography question maybe. I am using phenix.refine and I have a model structure refined against data at 3.4A. The model was built from experimental phasing. I reprocessed the same dataset, to include another angstrom resolution (3.3). It has 50% of the data from 3.4 to 3.3 and the I/sigI is about 2. When I refine my structure at 3.4 the stats are 32 and 36 for R and Rfree, but when I use the phase extended data (and the same reflections are the test set up to 3.4A as long as CCP4i did the job right with setting the Rfree) the stats suddenly jump to 49 and 56 when I refine the model against the higher resolution data. Is there something I am missing? I am doing a rigid and an anneal before individual sites and adp refinement. The space group is P3121. Regards Christine

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input initial TLS parameters
by iulek 24 Feb '08

24 Feb '08

Dear all, I tried to find a way to input initial TLS parameters for the groups into phenix. I know many times this is not advisable, but I wanted to test what comes out from TLSmd server. I could not find any reference on how to do this. Note that I know how to define the groups (a previous question in this bb), the point now is to input initial parameters (origin, T, L, S). Thanks, Jorge

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ligand refinement
by Christine Gee 22 Feb '08

22 Feb '08

Dear Phenix developers I have a covalently bound ligand in my structure and I would like to use phenix to refine the structure. The ligand is bound to the sulfur of a cysteine. What is the best method for defining the ligand. Should I generate a cif file for the whole amino acid and the ligand, or can I make one for just the ligand and add in some restraint somewhere which tells phenix to make a bond between the ligand atom and a nearby sulfur in a cysteine. If I generate a cif file with the whole amino acid and ligand, I assume I will I have to follow some convention in atom naming so that the main chain bonds and angles will form and refine OK? Regards Christine

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Phenix.refine Questions
by Mary Fitzgerald 22 Feb '08

22 Feb '08

First, I have a hopefully easy question. I can't seem to figure it out although feel like I should be able to. Is there a way to run a phenix.refine job in the background? I tried using the & like I usually do and it didn't work. It would be nice to start a job and go home without leaving myself logged into the computer. I didn't see anything in the documentation which makes me think I'm being dull. Second, a technical question. When phenix.refine does ordered solvent, does it use detwinned maps if you've put in the appropriate twin operator and indicated it was twinned? When I've tried running phenix.refine with my perfect twin, it doesn't seem to find waters like I can using the CNS twinned water picking script. Third, is it possible to run phenix.refine in parallel at all. My structure is annoying large and the parallelization of FFT in CNS seems to help speed things up abit. Thanks, Mary X. Fitzgerald Postdoctoral Associate Arnold Lab

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geometry in phenix.refine
by Jianghai Zhu 21 Feb '08

21 Feb '08

Hi, I recently noticed that the geometry in my structure is much worse than my previous model. Here are some examples. The RMSD results after a refinement by phenix 1.3b. stage angl bond chir dihe plan repu 3_bss: 0.711 0.009 0.059 18.282 0.002 3.917 after switching to cci version 2008_02_08_1610, I tried to do a geometry minimization by setting wxc_scale = 0. The RMSD I got from the previous model is as following. stage angl bond chir dihe plan repu 0 : 1.394 0.124 0.147 20.782 0.004 3.925 and after 6 macro cycles of geometry minimization, stage angl bond chir dihe plan repu 6_bss: 0.622 0.011 0.120 13.143 0.003 3.822 It funny that the RMSD are so different for the same model. What happened? Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D Immune Disease Institute Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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Re: [phenixbb] Phenix.refine Questions - specifically running Phenix in the background
by Edward Snell 21 Feb '08

21 Feb '08

Re: <quote> Message: 8 Date: Thu, 21 Feb 2008 14:23:24 -0500 From: "Mary Fitzgerald" <mary.x.fitzgerald(a)gmail.com> Subject: [phenixbb] Phenix.refine Questions To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Message-ID: <2fc50e280802211123h192c095x9c65f5bd6f1d4a55(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" First, I have a hopefully easy question. I can't seem to figure it out although feel like I should be able to. Is there a way to run a phenix.refine job in the background? I tried using the & like I usually do and it didn't work. It would be nice to start a job and go home without leaving myself logged into the computer. I didn't see anything in the documentation which makes me think I'm being dull. </quote> Apologies if someone has already answered this but you can set up a little command file e.g. 'refine.com', something along the lines of: phenix.refine model_from_coot.pdb data.mtz ligand.cif my_favourite.params --quiet With all your parameters in 'my_favourite.params' and run it with > nohup ./refine.com & You can then log off and check it later and it will still be running. The key seems to be the nohup and the '--quiet' switch. Works for me, hope it works for you. Cheers, Eddie Edward Snell Ph.D. Assistant Prof. Department of Structural Biology, SUNY Buffalo, Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Email: esnell(a)hwi.buffalo.edu Telepathy: 42.2 GHz Heisenberg was probably here!

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refining nucleic acids, formats?
by Green, Todd 20 Feb '08

20 Feb '08

Hello All- I'm trying to refine some RNA and I can't seem to get phenix to read in my pdb file as it seems to not recognize the the nucleic acid as nucleic acid, as opposed to protein. By comparison to another pdb from the rcsb site(3b31) I seem to be following the same convention. Any suggestions on what I am doing wrong? I do have protein in the pdb as well. The protein has a different chain id. I am running phenix-1.24.1b, my next move if I can't figure this out is to upgrade. Do I have the format of the RNA wrong? Here is the error message and below that is an example of the first residue of the rna. Cheers- Todd *********************************** sorry the PDB file xxx.pdb has an incomplete residue (or conformer/residue combination) in conformer '' chain R residue U 1 because this conformer is missing the following main-chain atoms: ['N', 'CA', 'C'] *********************************** ATOM 18243 O5' U R 1 50.409 12.832 14.548 1.00144.33 O ATOM 18244 C5' U R 1 49.763 12.566 15.794 1.00144.88 C ATOM 18245 C4' U R 1 49.745 13.804 16.678 1.00145.19 C ATOM 18246 O4' U R 1 49.036 13.579 17.920 1.00145.17 O ATOM 18247 C1' U R 1 49.400 14.624 18.811 1.00145.36 C ATOM 18248 N1 U R 1 49.443 14.148 20.242 1.00145.47 N ATOM 18249 C2 U R 1 48.886 14.949 21.229 1.00145.51 C ATOM 18250 O2 U R 1 48.347 16.024 21.005 1.00145.55 O ATOM 18251 N3 U R 1 48.976 14.439 22.507 1.00145.32 N ATOM 18252 C4 U R 1 49.555 13.242 22.895 1.00145.27 C ATOM 18253 O4 U R 1 49.558 12.920 24.081 1.00145.43 O ATOM 18254 C5 U R 1 50.118 12.468 21.816 1.00145.29 C ATOM 18255 C6 U R 1 50.045 12.940 20.562 1.00145.32 C ATOM 18256 C2' U R 1 50.735 15.197 18.331 1.00145.42 C ATOM 18257 O2' U R 1 50.561 16.545 17.935 1.00145.28 O ATOM 18258 C3' U R 1 51.102 14.243 17.192 1.00145.51 C ATOM 18259 O3' U R 1 51.827 14.863 16.146 1.00146.05 O

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workshop abstract
by Tom Terwilliger 19 Feb '08

19 Feb '08

Hi Peter he is an abstract for my talk. Thanks! -Tom T Phenix Wizards -- Automation of the Structure Determination Process The PHENIX Wizards allow automation of major steps in the structure determination process. The Wizards carry out decision-making, provide suggestions for the user, and form a flexible environment for investigating alternative strategies for structure determination. New algorithms available in PHENIX include a Iterative-build OMIT procedure for prevention of model bias and ligand identification in electron density maps. The PHENIX AutoBuild Wizard can carry out iterative model-building, density modification and refinement to improve the quality of models at resolutions as low as 3 Å. Electron density maps calculated using an atomic model can be affected by model bias introduced during refinement of the model. We have developed a Iterative-build OMIT procedure that prevents model bias in iterative procedures for model-building and refinement while producing a high-quality electron-density map. The PHENIX LigandFit automated ligand-fitting Wizard can fit flexible ligands into an electron density map. The Wizard can identify unknown ligands by comparing a set of potential ligands to the map and finding the one that fits the density most closely. Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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