- phenixbb - phenix-online.org

refinement problems
by Christine Gee 01 Mar '08

01 Mar '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

2 1

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

5 7

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

3 2

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

4 4

geometry in phenix.refine
by Jianghai Zhu 22 Feb '08

22 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 +++++++++++++++++++++++++++++++

4 16

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!

1 0

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

3 2

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

1 0

Re: [phenixbb] Clashes problem
by Pavel Afonine 13 Feb '08

13 Feb '08

Hi All, 1) phenix.refine has a standard set of geometry restrains as other refinement programs: bond, angle, planarity, chirality, dihedral, non-bonded. Clash score is not something that is included into refinement as a target and then used directly in refinement. Clash scores may be bad at the beginning of structure refinement and should be good at the end. 2) Using H atoms as a riding model should normally help in fixing clashes, however it's not 100% guaranteed: some clashes may be "locked" so the refinement cannot overcome the barriers even with H atoms. In this case what's Luca Jovine suggesting (see one of the emails in this thread) is an excellent thing to do (to add to his receipt: you may also consider using more than default number of macro-cycles). Running simulated annealing is also helpful (use "simulated_annealing=true" flag for this). 3) Since handling of H atoms in phenix.refine is significantly improved in newer versions, I would warmly recommend to use the latest phenix.refine available (currently from CCI Apps: http://www.phenix-online.org/download/cci_apps/). 4) Also, clashes related concerns may be a result of inoptimal weight between Xray target and restrains. Although one can play with the weight adjusting scales manually by trying different values of "wxc_scale" parameter ("wxu_scale" is analog for b-factors refinement) the new version of phenix.refine has an automatic procedure for finding the best weight (here "the best" means the weight that leads to the lowest Rfree) (Carsten's suggestion). To use this option: % phenix.refine model.pdb data.mtz your_parameters.par optimize_wxc=true Note this this may take a while to run (depending on resolution and structure size) so consider running it overnight. If none of the above helps, I would be *very* interested to look at the data and model myself to 1) help you find the best strategy to overcome this problem, and 2) find and fix problem in phenix.refine (if any). As always, I promise to keep all data confidential. Pavel.

4 5

alternative conformations
by Dr. Colin W. Levy 13 Feb '08

13 Feb '08

Hi, What is the correct procedure in phenix for dealing with alternative conformations of side chains? Thanks Colin

3 2

Clashes problem
by Simon Kolstoe 11 Feb '08

11 Feb '08

Dear Phenix community, I am using phenix.refine version 2007_08_18_1856 to refine a 2.65A structure (with individual_sites, group_adp, TLS & NCS, wxc_scale=0.1). After refinement I am running the pdb file through the Molprobity server. Molprobity gives a clash score of 33.78 indicating the number of steric clashes (within 0.4A) per 1000 atoms. I am slightly concerned that a refinement program seems happy to allow such clashes. Is this a problem with the version of phenix.refine I am running, or is there a more obvious explanation that I have missed? Thanks, Simon

7 7

Making GDP (non-polymer) into an RNA monomer
by Francis E Reyes 09 Feb '08

09 Feb '08

All I need to attach a 5' modification, a diphosphate guanosine to my RNA. I figure GDP (from the monomer library) has everything I need. However, what needs to be done to make a connection with the next nucleotide in the chain (in both phenix.refine and coot) ? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

2 3

Re: [phenixbb] Making GDP (non-polymer) into an RNA monomer
by Ralf W. Grosse-Kunstleve 09 Feb '08

09 Feb '08

Hi Francis, > However, what's the etiquette for how the residue should be named in > the PDB? I have it right now as GDP, though Gr seems much more > sensible? Or should I name it something completely custom? If the monomer library GDP matches what you have in the PDB I'd stick with the name. I'd rename the residue only if modifications are necessary. Gr would be a problematic alternative because the monomer library uses that already for RNA Guanosine (mon_lib/g/GR.cif). Ralf

1 0

Re: [phenixbb] lower case chain IDs
by Engin Ozkan 08 Feb '08

08 Feb '08

Thanks, Ralf. We will have the latest CCI Apps installed in our upcoming February software update (which should include your December update), and give it another try. That will probably fix it. Engin Quoting "Ralf W. Grosse-Kunstleve" <rwgk(a)cci.lbl.gov>: > Hi Engin, > >> which, I guess, is the CCI Apps version from August 2007. > > Yes, that explains it. Sorry, when I saw your first message > I should have thought of this immediately. > > To resolve your problem, you'll need the latest CCI Apps. > Multiple CCI Apps versions can co-exist and the installation > takes only seconds. Could you try that? > > http://www.phenix-online.org/download/cci_apps/ > > You can install it under your home directory, i.e. you don't need > special privilleges. > Just make sure you source the setpaths of the version you want to use. > > Ralf >

1 0

lower case chain IDs
by Engin Ozkan 08 Feb '08

08 Feb '08

Hi everyone, We have a case with 32 molecules/asu, and have been using lower-case chain IDs. But we could not figure out how to describe lower-case chain IDs for NCS purposes? In CNS, quotation marks around the segID in ncs.def does it, but that trick does not seem to work in phenix.refine. Thanks, Engin

2 1

A few questions
by Rife, Christopher L 07 Feb '08

07 Feb '08

Hi, We are working on a refinement at 1.14A which was suffering from lots of NPD atoms when refined anisotropically with refmac5 and/or shelx. We followed the guidelines recently posted to this BB, and initially the results looked pretty good, but upon close inspection we have a few questions. We are using Version: 2008_01_09_2058. 1. In our model we have a few solvent ligands, and these show up in the log file as: Unusual residues: {'EDO': 11, ' CL': 1, 'SO4': 1} Classifications: {'undetermined': 13, 'water': 437} We've used a cif file for EDO with H's when needed, but still see this message. Is this normal? What is unusual? 2. When choosing "indivdual_occupancies" for the refinement, all the atoms within an alt-conf are refined to different occupancies- is this expected? It seems that all atoms in the A conf should have the same value, and the occ of all atoms in the B conf should also be the same. Instead, we see this: ATOM 232 CA AGLU A 28 26.163 7.163 4.422 0.77 6.73 C ATOM 233 CB AGLU A 28 24.851 7.269 3.672 0.80 9.27 C ATOM 234 CG AGLU A 28 24.978 6.767 2.259 0.66 12.91 C ATOM 235 CD AGLU A 28 23.662 6.717 1.554 1.00 16.51 C ATOM 236 OE1AGLU A 28 22.874 7.667 1.757 0.71 18.78 O ATOM 237 OE2AGLU A 28 23.429 5.733 0.803 0.60 16.77 O ATOM 240 CA BGLU A 28 26.140 7.156 4.424 0.23 6.33 C ATOM 241 CB BGLU A 28 24.794 7.230 3.713 0.20 6.48 C ATOM 242 CG BGLU A 28 24.877 6.766 2.280 0.34 6.55 C ATOM 243 CD BGLU A 28 23.536 6.702 1.598 0.00 7.53 C ATOM 244 OE1BGLU A 28 23.497 7.014 0.381 0.29 7.85 O ATOM 245 OE2BGLU A 28 22.543 6.341 2.280 0.40 8.40 O 3. Adding hydrogens during anisotropic refinement results in the Parvati server giving "Illegal Biso" errors for many of the hydrogens. I can make the files available if that will help. Thanks, Chris ----------------------------------------- Structure Determination Core Joint Center for Structural Genomics Stanford Synchrotron Radiation Laboratory

9 14

Re: [phenixbb] Question/enhancement request for automated datafile conversion
by Ralf W. Grosse-Kunstleve 07 Feb '08

07 Feb '08

Hi Carsten, > The .sca file (or dtrek .ref) file gets automatically converted to a > mtz file with I-obs and SIGI-obs and refinement proceeds as expected. I > just noticed that in the following ...002.def file and in the 001.eff > file the parameter xray_data.observation_type is set to amplitude > instead of intensities. What is going on there, is phenix smart enough > to know when it deals with amplitudes vs. intensities? Did not seem to > have much effect on the refinement though when I switched this around, > which is surprising. That parameter wasn't actually used. I just removed it completely. Thanks for alerting us to this. > As an enhancement request: Would it be possible that the autoconversion > writes out a mtz file which contains BOTH amplitudes and intensities > instead of intensities and R-flags alone? OK, done! You will see the change in the next release (hopefully very soon). Ralf

1 0

Question/enhancement request for automated datafile conversion
by Schubert, Carsten [PRDUS] 06 Feb '08

06 Feb '08

Hi, I noticed that there is a possible inconsistency in the handling of xray datafiles in phenix. For instance, we usually invoke phenix like this: phenix.refine my.sca my.pdb my.def The .sca file (or dtrek .ref) file gets automatically converted to a mtz file with I-obs and SIGI-obs and refinement proceeds as expected. I just noticed that in the following ...002.def file and in the 001.eff file the parameter xray_data.observation_type is set to amplitude instead of intensities. What is going on there, is phenix smart enough to know when it deals with amplitudes vs. intensities? Did not seem to have much effect on the refinement though when I switched this around, which is surprising. As an enhancement request: Would it be possible that the autoconversion writes out a mtz file which contains BOTH amplitudes and intensities instead of intensities and R-flags alone? Sometimes it happens that I need to go back to running phaser when the initial rigid body refinement does not grip. Since phaser just runs on amplitudes I need to add a couple of extra steps to get a file, which is useful for both programs. I think the underlying philosophy should be that once data has been imported into the phenix suite, from whichever entry point, it should be usable w/o conversion in all applications. Cheers, Carsten

1 0

Question abount B-factor refinement - B-factors = 0
by Schubert, Carsten [PRDUS] 04 Feb '08

04 Feb '08

Hi, I have a question about B-factor refinement in phenix. This is a reiteration of one or two of threads with the same subject dating back to September last year: Initially, I noticed that the B-factors within a residue have quite a large spread, when one runs a temperature factor variance analysis as implemented in coot (Yes I read Pavel's response about this ...). This prompted me to actually look at the B-factors in the PDB file. I noticed that actually for quite a few residues one or more of the B-factors refines to 0.00 For instance one of the less extreme examples: ATOM 118 N HIS A 21 -28.768 35.430 2.317 1.00 4.73 N ATOM 119 CA HIS A 21 -27.357 35.565 2.625 1.00 0.00 C ATOM 120 C HIS A 21 -27.124 35.408 4.116 1.00 2.25 C ATOM 121 O HIS A 21 -28.072 35.360 4.902 1.00 7.73 O ATOM 122 CB HIS A 21 -26.853 36.940 2.186 1.00 8.10 C ATOM 123 CG HIS A 21 -27.610 38.078 2.799 1.00 11.18 C ATOM 124 ND1 HIS A 21 -28.733 38.624 2.216 1.00 17.18 N ATOM 125 CD2 HIS A 21 -27.418 38.759 3.955 1.00 13.28 C ATOM 126 CE1 HIS A 21 -29.194 39.600 2.979 1.00 25.70 C ATOM 127 NE2 HIS A 21 -28.414 39.701 4.041 1.00 12.79 N As background the data extends to 1.8A, with an I/I(s) of ~15 and ~2.5 in the highest shell, CHI^2 are all around 1+/ 0.1. The Wilson B is 11.3A^2 and R/Rfree 16.8/19.8%. This is homesource date, at the synchrotron I could probably push the resolution further out to better than 1.6A. No hydrogens were added, nor was TLS used. In order to get around the problem I initally reset all B-values to the Wilson-B, enabled wxc refinement (latest CCI-APPs) and refined ADPs only for 10 macrocycles. After a couple of cycles the B-factor distribution settled into the following, which looks fairly reasonable to me, except for the min values of 0.00: |-ADP statistics (Wilson B = 11.289)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 2659 0 0.00 129.99 13.58 None None None | | all(noH): 2659 0 0.00 129.99 13.58 None None None | | Sol. : 390 0 0.35 56.99 27.75 None None None | | Mac. : 2269 0 0.00 129.99 11.14 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 0.000 - 12.999: 1778 | 5: 64.993 - 77.991: 17 | | 1: 12.999 - 25.997: 492 | 6: 77.991 - 90.990: 9 | | 2: 25.997 - 38.996: 210 | 7: 90.990 - 103.988: 4 | | 3: 38.996 - 51.994: 124 | 8: 103.988 - 116.987: 2 | | 4: 51.994 - 64.993: 19 | 9: 116.987 - 129.985: 4 | | =>continue=> | |-----------------------------------------------------------------------------| B-factors of 0 indicate to me that there is a problem, not sure how to tackle this in phenix at this point. Could there be a problem with the bulk-solvent scaling? Should I restrict the minimum B-factor to 1.0 (ugggh)? Or should I tighten the B-factor restraints? Cheers, Carsten

2 3

Re: [phenixbb] Maps from twinned data
by Peter Zwart 04 Feb '08

04 Feb '08

Hi Mary, Can you try and download the latest cci_apps and recompute the maps with phenix.refine? I did make some updates since rc6 in the dewtinning code. Cheers Peter 2008/2/1, Mary Fitzgerald <mary.x.fitzgerald(a)gmail.com>: > Peter- > I've attached an image from coot. I loaded my model and then a cns > detwinned 3fo-2fc map (purple) and the 2fo-fc (blue) from phenix both are > contoured at 1.5. The 3fo-2fc is the only map have at the moment equivalent > to the 2fo-fc model although it had waters in the model. I have the > symmetry brought up and there's not a symmetry related molecule in the area. > I've been working with this model quite a while and have never seen density > there before. It shows up in a couple of other spots as well with nothing > appearing in the fo-fc maps, which I didn't show here. It looks as if I'm > missing part of my model in areas that there shouldn't be any model. > > Thanks, > Mary > > > On Feb 1, 2008 2:59 PM, Peter Zwart <PHZwart(a)lbl.gov> wrote: > > Can you send a picture of the density and/or the data and model so I > > can have a look. > > The detwinning is done differently and for twin fractions of 0.5 > > something weird mihgt be happening. > > > > Thanks > > > > Peter > > > > > > > > > > 2008/2/1, Mary Fitzgerald <mary.x.fitzgerald(a)gmail.com>: > > > > > > > > > I'm new to phenix and just installed Phenix 1.3 beta rc6. > > > > > > I've taken a data set that I've been refining in cns and am trying > > > phenix.refine. The data has a twinning fraction of 0.5. I'm seeing > what I > > > think is odd in the 2mFobs-DFmodel.map. If I'm reading the > documentation > > > correctly, this map should be detwinned (I also set > > > > refinement.twinning.detwin.map_types.aniso_correct=true), I > > > see alot of extra density where there is no model, nor a symmetry > related > > > molecule in coot. I don't see this extra density in my detwinned 2fofc > cns > > > maps. > > > > > > So, could the extra density I'm seeing be due to using a different > program > > > and it is detwinning the data differently. The extra density is from > the > > > twin???? > > > > > > Any input would be appreciated, > > > > > > Mary X. Fitzgerald > > > Postdoctoral Associate > > > Arnold Lab > > > > > > > > > _______________________________________________ > > > phenixbb mailing list > > > phenixbb(a)phenix-online.org > > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > > > > > > > >

2 1

Maps from twinned data
by Mary Fitzgerald 01 Feb '08

01 Feb '08

I'm new to phenix and just installed Phenix 1.3 beta rc6. I've taken a data set that I've been refining in cns and am trying phenix.refine. The data has a twinning fraction of 0.5. I'm seeing what I think is odd in the 2mFobs-DFmodel.map. If I'm reading the documentation correctly, this map should be detwinned (I also set refinement.twinning.detwin.map_types.aniso_correct=true), I see alot of extra density where there is no model, nor a symmetry related molecule in coot. I don't see this extra density in my detwinned 2fofc cns maps. So, could the extra density I'm seeing be due to using a different program and it is detwinning the data differently. The extra density is from the twin???? Any input would be appreciated, Mary X. Fitzgerald Postdoctoral Associate Arnold Lab

1 0

phenix.refine & twin fraction
by Karolina Michalska 29 Jan '08

29 Jan '08

Dear all, Can onyone tell me how to introduce twin fraction to the refinement parameters? According to phenix.xtriage it should be 0.4 but phenix.refine uses 0.2. Thanks a lot, Karolina -- *********************************** Karolina Michalska, PhD Dept. of Crystallography Faculty of Chemistry A. Mickiewicz University ul. Grunwaldzka 6 60-780 Poznan, Poland ***********************************

2 1

Re: [phenixbb] phenix.find_ncs and DANO
by Tom Terwilliger 24 Jan '08

24 Jan '08

Hi Bryan, >in principle, phenix.find_ncs should be fine with FP=DANO, right? I'm not quite clear on this, but yes, find_ncs wants a map, and you can give it any map coefficients with labin="labin FP=FP PHIB=PHIB FOM=FOM " >and - do i understand correctly that phenix only correlates the map with >the .pdb sites, and does not rotate the map about itself (like in getax, i >think)? Correct, find_ncs is looking for NCS in the heavy-atom sites as presented in a PDB file, or in a model as given in a PDB file, without rotating the map. Any crystallographic symmetry is automatically applied. >-bryan > >p.s: > >i can run phenix.find_ncs with FP=DANO, but seems that resolve wants it to >be FP as usual. It might be helpful if you could send me this example! I hope that helps! -Tom T 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

1 0

high resolution refinement with phenix.refine
by Pavel Afonine 22 Jan '08

22 Jan '08

Dear phenix.refine users: responding to Vijayalakshmi Janakiraman's questions about refinement at high resolution with phenix.refine, I finally documented this functionality of phenix.refine and supplied it with a small example. This paragraph (see attached HTML file) will be available as part of phenix.refine documentation in the next release of PHENIX and CCI Apps. *Important:* writing this text I assumed that the latest version of phenix.refine is used (currently, it is one from CCI Apps: /2008_01_09_2058/ , http://www.phenix-online.org/download/). Cheers, Pavel. >> I have a high resolution structure with NADP as ligand bound to it. >> I was using CNS to start with. Somehow the Rfree was always very >> high. But when I tried with default options of data= and model=, >> in phenix.refine with the whole data and the intial rigid body >> refined coordinates from CNS, the Rfactors came down to 31%. I have >> now decided to do refinements with phenix.refine. >> Do you suggest any protocol for refinement of structure at this high >> resolution starting from initial rigid body refinements? >> Since I would like to handle alternate conformations in the final >> steps. I am wondering if the 2007 July version could handle >> refinements of alternate conformations. >> Thanks, >> Viji

1 0

Re: [phenixbb] Autosol Feedback and questions
by Tom Terwilliger 22 Jan '08

22 Jan '08

Hi Partha, At 03:53 AM 1/2/2008, you wrote: >Happy new year everybody, > >I had quite a bit of difficulty with a SAD dataset which also showed >Sulphur. Previously I had tried SHELEX to find sites, MLPHARE to >refine, AddSOLVE to find more , and both SOLVE and PHASER to solve >but it did not get to a point where I could do manual building. >Autosol worked beautifully, the input files were scalepack merged >data, ha.pdb (from addsolve step), and the sequence. PHASER to solve >and TEXTAL & RESOLVE with through build option. > >This actually leave me with some confusions / questions: > >1. When I compare the other "solutions", they look like the right >one, just not good enough. Where exactly is the autosol making a >difference? Is it the ability of of TEXTAL to build something more >meaningful when the solution is not good or number of iterations? Autosol uses the quality of the model built as a score, if any model is built (R-factor if < 0.40; number of residues built less 2 * number of chains otherwise).. If no model is built, it uses the standard 4 or 5 criteria that are printed out on the AutoSol wizard screen (CC and R-factor for density modification; skew of electron density histograms, FOM, CC of NCS). >2. How does PHASER know the different anomalous atoms? Does is use a >different scaling factor for SE and S? It can tell by the ratio of anomalous to real scattering corresponding to each atom. >3. I see that phenix.refine has been used in the internal runs, I >have used phenix.refine earlier. But after playing with the side >chains in Coot, when I tried to use the modified pdb file and >resolve.mtz, it complained about the good old Free_R flag. However, >it ran directly in Refmac. Is it a known problem or maybe I did >something stupid? I could do a dry run and change the read mtz and >not cns if that would solve the problem. As Pavel and Ralf have mentioned, this is because AutoSol has tossed a few (usually blank) reflections from your reflection file when it created the refinement file exptl_fobs_phases_freeR_flags_15.mtz # or something similar. Without the "_15" if from AutoBuild The solution is to either (1) use the refinement file from AutoSol (exptl_fobs_phases_freeR_flags_15.mtz), or to delete the MD5 remark record from the AutoSol/AutoBuild PDB file. >4. Lastly, is it possible to use multiple processors to run the job? As Pavel mentioned...we are thinking about this but do not have anything yet. -Tom T 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

1 0

Re: [phenixbb] Continue from an AutoBuild job abruptly killed
by Tom Terwilliger 22 Jan '08

22 Jan '08

Hi Miguel, I'm sorry for the slow response...you can continue AutoBuild by typing: phenix.autobuild run=1 if you were previously on run #1 and you want to continue it. All the best, Tom T At 02:24 AM 1/16/2008, you wrote: >Dear all, > >We had a problem with a machine running >AutoBuild, which resulting in the computer going >down and the AutoBuild job consequently killed. >I've tried to find out if there is a way to >continue the job (it had been running for four >days and still had a few hours to go I guess: a >pretty big unit cell) but I failed. I would >appreciate if someone could point to the >relevant pages in the manual/tutorials or give >me advice about how to do such a thing. If that's possible, of course. > >We're using the latest phenix (1.3b-rc6) and cci apps. > >Thank you! > > >Miguel >-- ><http://www.pangea.org/mol/spip.php?rubrique2>http://www.pangea.org/mol/spip.php?rubrique2 > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >Je suis de la mauvaise herbe, >Braves gens, braves gens, >Je pousse en liberté >Dans les jardins mal fréquentés! > >Georges Brassens >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb 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

1 0

Re: [phenixbb] picking Rfree set
by Peter Zwart 22 Jan '08

22 Jan '08

yes, it will. This is useful for when the data is twinned. P 2008/1/22, David Garboczi <dgarboczi(a)niaid.nih.gov>: > So, for instance, when addition of a ligand to a P212121 cell (1 mol) > changes the symmetry to P21 (almost same cell, but 2 mol), the > selection of the Rfree set from the P21 data by phenix.refine will > take the higher almost symmetry into account? > > Dave > > >btw3: the lattice symmetry is taken into account when choosing an free > >set in phenix.refine (unless specified otherwise). If all NCS > >rotational operators are approximately parallel to twin laws, you > >should be fine. > > > >P > > > > > > > > > > > >2008/1/22, Ralf W. Grosse-Kunstleve <rwgk(a)cci.lbl.gov>: > >> > Does phenix.refine take NCS into account when picking the Rfree set? > >> > Thin shells, or other strategy... > >> > >> The short answer is no. > >> We had long internal discussions about this without reaching a final > >> conclusion. In the long run we may integrate alternative R-free set > >> distributions in phenix.refine; in the meantime you have to use > >> an external program (e.g. dataman or sftools). > >> BTW 1: just to prove that we have thought about this subject, we have a > >> simple tool for "visualizing" distributions of R-free flags: > >> iotbx.r_free_flags_accumulation your.mtz > >> It writes a file with x,y pairs which you can plot with e.g. Excel > >> or any other 2D plotting program. > >> BTW 2: The free reflections aren't as free as one may think. When > >> using a maximum likelihood target (any program), the free reflections > >> are used in the estimatation of the error model. This estimation > >> becomes more tricky if the reflections are distributed in thin > >> shells. I.e. if you go to thin shells you may in fact account to some > >> degree for the NCS, but at the same time you compromise the error > >> model estimation. > >> Ralf > >> _______________________________________________ > >> phenixbb mailing list > >> phenixbb(a)phenix-online.org > >> http://www.phenix-online.org/mailman/listinfo/phenixbb > >> > >_______________________________________________ > >phenixbb mailing list > >phenixbb(a)phenix-online.org > >http://www.phenix-online.org/mailman/listinfo/phenixbb > > > -- > David N. Garboczi, PhD > Phone: 301-496-4773 > Investigator, Structural Biology Section (SBS) > Laboratory of Immunogenetics (LIG) > National Institute of Allergy and Infectious Diseases (NIAID) > National Institutes of Health (NIH) > Twinbrook 2/Room 110 > 12441 Parklawn Drive > Rockville, Maryland 20852-1742 > Fax: 301-402-0284 > Email: dgarboczi(a)niaid.nih.gov > > > > > 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. The National Institute > of Allergy and Infectious Diseases (NIAID) shall not accept liability > for any statement made that are the sender's own and not expressly made > on behalf of the NIAID by one of its representatives. > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

2 1

picking Rfree set
by David Garboczi 22 Jan '08

22 Jan '08

Does phenix.refine take NCS into account when picking the Rfree set? Thin shells, or other strategy... Dave --

3 3

Re: [phenixbb] autosol : input_ncs_file
by Tom Terwilliger 22 Jan '08

22 Jan '08

Hi Bryan, No, autosol does not let you tell it what the NCS is with input_ncs_file. This is a good idea, however... -Tom T At 06:45 PM 1/15/2008, you wrote: >using PHENIX VERSION: 1.3b of 20-11-2007. > >does phenix.autosol use "input_ncs_file"? > >the documentation implies that phenix.autosol will take `input_ncs_file` >(at the 'find_ncs' entry, "input_ncs_file" is mentioned but no where >else), yet, i get a 'Sorry, unknown file or keyword:' message with no such >command line option listed. > >-bryan >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb 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

1 0

modify_start_model.adp.set_b_iso doesn't seem to work on PDB files with ANISOU cards
by Stephen Graham 21 Jan '08

21 Jan '08

Hi all, I just tried to reset my B values to the wilson B before TLS refinement (in an attampt to shake some model bias that I am sure is hiding somewhere in my temperature factors...). My start model was a TLS-refined PDB file from phenix.refine (hence with ANISOU cards). I issued the following command: > phenix.refine my_model.pdb my_data.mtz modify_start_model.adp.set_b_iso=60 output.prefix=my_model_resetB main.number_of_macro_cycles=0 As far as I can tell, this should reset my B values to 60 and then exit. However, when I look at the resultant PDB file the Bs for all the solvent molecules 60 but for the protein they are not; rather the protein Bs are almost identical to the starting PDB file. If I try to remove the TLS-derived ANISOU cards by adding the command line option "adp.convert_to_isotropic=true" the result is the same (except the output PDB file no longer has ANISOU cards). However, if I strip out the ANISOU cards from my starting pdb file and _then_ run the above command the resultant PDB file _does_ have the correct values for both protein and solvent. It seems like modify_start_model.adp.set_b_iso=60 does not work when atom has an ANISOU card. The behaviour I would *expect* would be for the adp be reset to an 'isotropic' 60 (i.e. set the diagonal elements to 1 and the off-diagonals to 0). Is this a bug, or am I doing something silly? Cheers, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

3 3

d_min_textal=
by Bryan W. Lepore 19 Jan '08

19 Jan '08

the documentation says : "Textal has an optimal high-resolution limit of 2.8 A" is that to say that resolutions != 2.8 are not optimal? -bryan

2 1

Re: [phenixbb] disulfide bonds in phenix.refine
by Ralf W. Grosse-Kunstleve 18 Jan '08

18 Jan '08

Hi Allister, > 1) How do I specifically prevent a disulfide bond from being defined > between two sulfurs that are close together (I tried manipulating the > "disulfide_distance_cutoff" variable but this doesn't seem to stop a > disulfide being formed). If you set, e.g. disulfide_distance_cutoff=0.1 you shouldn't get any disulfide bonds anymore. I just tried it on a small structure and it worked as expected. > 2) How can I soften the restraint on the disulfide bond length for > specific cysteine residues. With the current phenix.refine you cannot edit the automatically determined disulfide bonds (sorry). However, you can use disulfide_distance_cutoff=0.1 to turn off the automatic bonds. Then use geometry_restraints.edits (see documentation at http://phenix-online.org/documentation/refinement.htm) to define the disulfides manually one by one, with the ideal distances and sigmas you want to use. Use a log file from a previous phenix.refine run to obtain the list of all disulfides. Ralf

1 0

disulfide bonds in phenix.refine
by Allister.Crow＠uea.ac.uk 18 Jan '08

18 Jan '08

Hello all, I am currently trying to refine a structure (with phenix.refine) that contains a number of disulfide bonds. Many of these disulfides appear to be partly broken such that the default restraints given to these disulfides by phenix.refine cause the cysteine sulfur atoms to be placed too close to one another. This results in difference density in the fo-fc map. I want to try to model these partially broken states a bit more accurately, either by modelling two alternative conformations (i.e. one cysteine pair in a disulfide and the other pair as free thiols) or by allowing the disulfide bond distance to stretch. Currently refinement drives the S-S bond length close to dictionary values regardless of how far apart I model the cysteines in my input pdb file and whether the density implies a bridge or not. My two questions are: 1) How do I specifically prevent a disulfide bond from being defined between two sulfurs that are close together (I tried manipulating the "disulfide_distance_cutoff" variable but this doesn't seem to stop a disulfide being formed). 2) How can I soften the restraint on the disulfide bond length for specific cysteine residues. Thanks for your time. Dr. Allister Crow

1 0

Continue from an AutoBuild job abruptly killed
by Miguel Ortiz-Lombardía 17 Jan '08

17 Jan '08

Dear all, We had a problem with a machine running AutoBuild, which resulting in the computer going down and the AutoBuild job consequently killed. I've tried to find out if there is a way to continue the job (it had been running for four days and still had a few hours to go I guess: a pretty big unit cell) but I failed. I would appreciate if someone could point to the relevant pages in the manual/tutorials or give me advice about how to do such a thing. If that's possible, of course. We're using the latest phenix (1.3b-rc6) and cci apps. Thank you! Miguel -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens

2 3

MSE gap
by Troy E Messick 16 Jan '08

16 Jan '08

Hello, I seem to be having a problem with phenix.refine and the seleno-methionine residue (resname MSE). It seems that I have a gap in the peptide bond between the C atoms and the N atom of the subsequent residue. Is there something I could add to the restraints_edits.params file to get it to click together? What is the distance_ideal and sigma for a peptide bond? Thanks for your help, Troy

4 7

phenix.find_ncs and DANO
by Bryan W. Lepore 16 Jan '08

16 Jan '08

in principle, phenix.find_ncs should be fine with FP=DANO, right? and - do i understand correctly that phenix only correlates the map with the .pdb sites, and does not rotate the map about itself (like in getax, i think)? -bryan p.s: i can run phenix.find_ncs with FP=DANO, but seems that resolve wants it to be FP as usual.

1 0

autosol : input_ncs_file
by Bryan W. Lepore 16 Jan '08

16 Jan '08

using PHENIX VERSION: 1.3b of 20-11-2007. does phenix.autosol use "input_ncs_file"? the documentation implies that phenix.autosol will take `input_ncs_file` (at the 'find_ncs' entry, "input_ncs_file" is mentioned but no where else), yet, i get a 'Sorry, unknown file or keyword:' message with no such command line option listed. -bryan

1 0

strategy of refinement for a structure phased by bromide soaking
by Pascal EGEA 11 Jan '08

11 Jan '08

Dear All, I have a 1.8A resolution data set of a protein collected on a crystal soaked in KBr and I am solving using Phenix. I used AutoSol and gave a rough estimate of f_prime and f_double_prime for the Br scatterer as a starting point. It worked great and Phenix found 31 Bromide ions (only one is fully occupied) and the resulting map is remarkably clear. Automatic building has done a great job and I was able to build most of the 4 monomers present in the AU. However I am confused and have a couple of questions. 1-As Phenix started it generated a fobs_experimental_phases_free_Rflag.mtz file. I have been using this file and no longer my data.hkl file for further refinement. I would like to know why the best_solution after the automatic building run does not contain any of the Bromide ions. It has water molecules but no Bromide ions? What is the reason for that? 2-I have been refining against the mtz file I mentioned but without any of these Bromide ions and although the refinement is converging , I suspect I have been doing something bad and wrong. Should I start my refinement again from the first best pdb after automatic building and include right away the bromide ions with simultaneous f_prime, f_double_prime and occupancy refinement for the anomalous scatterers? As it stands now the Rfree is 22.9 and the Rfac is 19.7. The map looks fine except for the solvent, some of this atoms are obviously bromide and there is extra density in the Fo-Fc around some "solvent" atoms. Thanks a lot in advance for your suggestions. Pascal Egea University of California San Francisco Department of Biochemistry and Biophysics

4 3

iotbx.shelx.from_ins
by Foelker, Andrew 10 Jan '08

10 Jan '08

Hello Perhaps one of you could assist me with this question. In the from_ins.py file, there is a function by the name of from_ins. I am passing a .RES file to this function, but am not passing any of the other optional arguments to it. When line 51 in the file is reached, an exception is thrown. Here is the line of code that blows up: b = record.tempFactor + record_next.tempFactor The exception correctly states that the record_next object has no attribute named 'tempFactor'. Perhaps I am doing something incorrectly, or perhaps there is a bug in the from_ins function itself. If any of you can offer some insight into this problem I would greatly appreciate it. Thank you. ------------------------------------------------------------------------ -------- Andrew J. Foelker Software Engineer Bruker AXS Inc. 5465 E. Cheryl Parkway Madison, WI 53711 Tel: +1 608-276-3812 andrew.foelker(a)bruker-axs.com www.bruker-axs.com <http://www.bruker-axs.com/> ------------------------------------------------------------------------ ----------

2 4

Reading Rfree Flags from Refmac
by James Fraser 09 Jan '08

09 Jan '08

Hello, Someone in our lab has started a refinement run in REFMAC and wants to continue it in Phenix.refine. Is there an easy way to get phenix to recognize the r-free flag from REFMAC (freeR=0)? Thanks, jf -- James Fraser jamesfraser(a)berkeley.edu Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

2 2

Failure when calculating a composite omit map
by Dale Tronrud 07 Jan '08

07 Jan '08

Hi all, I'm trying to calculate a composite omit map so that I can get a clear view of a troublesome region in my structure. I have two copies of everything in the asu so I created some dummy atoms to mask the region in the A chain and called those atoms chain Y and another collection to mask the region in the C chain and created a Z chain for them. I put these atoms in a file name Mask.pdb I attempted to calculate the composite omit map starting from my MR solution but that fails because Autobuild doesn't like being given the Fourier coefficients produced by Phaser. To work around this problem I decided to ask it to create the omit map based on the results of my AutoBuild followed the MR. My script is: phenix.autobuild model=AutoBuild_run_12_/overall_best.pdb data=1M50-2.mtz \ input_refinement_labels="FP SIGFP None None None None None None FreeR_flag" \ seq_file=../fmo-ct.pir \ resolution=2.2 dmax=20 refinement_resolution=2.2 \ cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif \ input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \ composite_omit_type=iterative_build_omit omit_region_specification=omit_around_pdb omit_box_pdb=Mask.pdb\ omit_res_start_list="1 1" omit_res_end_list="39 30" omit_chain_list="Y Z" \ rebuild_in_place=Yes Mask.pdb is attached. Resolve is unable to create a mask. The log file, omit_box_id.log is also attached. Resolve creates a temp file named TMP.pdb which I would expect to contain the contents of my Mask.pdb. It only contains the first set of dummy atoms; chain Y. Then when Resolve reads this file it appears not to find even those atoms. I know Tom is out of reach for quite a while. Is there someone else who could help me over this hurdle? Dale Tronrud

1 0

Autosol Feedback and questions
by Partha Chakrabarti 04 Jan '08

04 Jan '08

Happy new year everybody, I had quite a bit of difficulty with a SAD dataset which also showed Sulphur. Previously I had tried SHELEX to find sites, MLPHARE to refine, AddSOLVE to find more , and both SOLVE and PHASER to solve but it did not get to a point where I could do manual building. Autosol worked beautifully, the input files were scalepack merged data, ha.pdb (from addsolve step), and the sequence. PHASER to solve and TEXTAL & RESOLVE with through build option. This actually leave me with some confusions / questions: 1. When I compare the other "solutions", they look like the right one, just not good enough. Where exactly is the autosol making a difference? Is it the ability of of TEXTAL to build something more meaningful when the solution is not good or number of iterations? 2. How does PHASER know the different anomalous atoms? Does is use a different scaling factor for SE and S? 3. I see that phenix.refine has been used in the internal runs, I have used phenix.refine earlier. But after playing with the side chains in Coot, when I tried to use the modified pdb file and resolve.mtz, it complained about the good old Free_R flag. However, it ran directly in Refmac. Is it a known problem or maybe I did something stupid? I could do a dry run and change the read mtz and not cns if that would solve the problem. 4. Lastly, is it possible to use multiple processors to run the job? Best regards, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

2 1

Re: [phenixbb] Using the Same Test Set in AutoBuild and Phenix.Refine
by Thomas C. Terwilliger 03 Jan '08

03 Jan '08

Hi Dale, Can you try something else: phenix.refine AutoBuild_run_12_/overall_best.pdb \ refinement.input.xray_data.file_name=\ AutoBuild_run_12/exptl_fobs_freeR_flags.mtz \ refinement.main.high_resolution=2.2 refinement.main.low_resolution=20 \ /usr/users/dale/geometry/chromophores/bcl_tnt.cif This differs from your run only by substituting AutoBuild_run_12/exptl_fobs_freeR_flags.mtz for your 2 refinement data files. This is the exact file that is used in refinement by AutoBuild. I agree that you should be able to use your original data file instead. A possible reason why this has failed is that the original data file has a couple reflections for which there is no data...and which were tossed by AutoBuild before creating exptl_fobs_freeR_flags.mtz . Two files that differ only in reflections with no data will still give different checksums, I think. All the best, Tom T > Hi Dale, > >>> 1) Why you specify reflection MTZ file twice in phenix.refine script? >>> >>> >> I put the mtz in twice because if I put it in once phenix.refine >> complains that I have no free R flags. It seems to want one file with >> the amplitudes and another with the flags. Since I have both in the >> same file I put that file on the line twice and phenix.refine finds >> everything it needs. >> > > phenix.refine looks for free-R flags in your main data file > (1M50-2.mtz). Optionally you can provide a separate file containing > free-R flags (I have to write about this in the manual). However, if > your 1M50-2.mtz contains free-R flags then you don't need to give it > twice. So clearly something is wrong at this step and we need to find > out what is wrong before doing anything else. Could you send the result > of the command "phenix.mtz.dump 1M50-2.mtz" to see what's inside of your > data file? Or I can debug it myself if you send me the data and model. > >> If the MD5 hash of the test set depends on the resolution then >> certainly >> I could be in trouble. > > No. It must always use the original files before any processing. > >> Does the resolution limit affect the MD5 hash of the test set? >> > > No. If it does then it is a very bad bug. I will play with this myself > later tonight. > >> >>> 3) Does this work: >>> >>> (...) >> >> I'll try these but it will take a bit of time. >> > > Don't run it until completion. Just make sure it passed through the > processing step. > > Pavel. > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

3 2

Using the Same Test Set in AutoBuild and Phenix.Refine
by Dale Tronrud 03 Jan '08

03 Jan '08

Hi all, I have another problem, I'm afraid. I have built a model using phenix.autobuild and now want to run some refinement. While in the long run I'll do some manually rebuilding using Coot I just wanted to run a test of phenix.refine to ensure I have the script right and have a baseline to compare against later. My autobuild script is: phenix.autobuild model=AutoMR_run_4_/MR.1-protein.pdb data=1M50-2.mtz \ input_refinement_labels="FP SIGFP None None None None None None FreeR_flag" \ map_file=AutoMR_run_4_/MR.MAP_COEFFS.1.mtz \ seq_file=../fmo-ct.pir \ resolution=2.2 dmax=20 refinement_resolution=2.2 \ cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif \ input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \ rebuild_in_place=Yes My refine script is phenix.refine AutoBuild_run_12_/overall_best.pdb \ refinement.input.xray_data.file_name=1M50-2.mtz 1M50-2.mtz \ refinement.main.high_resolution=2.2 refinement.main.low_resolution=20 \ /usr/users/dale/geometry/chromophores/bcl_tnt.cif As you can guess, my test set flags are in the same mtz file as the amplitudes. I'm feeding exactly the same file into both runs. Despite this I get in my output ******************************************************************************* ******************************************************************************* The MD5 checksum for the R-free flags array summarized above is: 785fd03f6881898dcd91bc5f8c3e5b26 The corresponding MD5 checksum in the PDB file summarized above is: 6f86ee71dbcd2dc1f5282cf18547c79b These checksums should be identical but are in fact different. This is because the R-free flags used at previous stages of refinement are different from the R-free flags summarized above. As a consequence, the values for R-free will be biased and misleading. It is best to avoid this situation by consistently using the same R-free flags throughout the refinement of a model. If the previously used R-free flags are still available run this command again with the name of the file containing the original flags as an additional input. If the original R-free flags are unrecoverable, remove the REMARK r_free_flags.md5.hexdigest 6f86ee71dbcd2dc1f5282cf18547c79b record from the input PDB file to proceed with the refinement. In this case the values for R-free will become meaningful only after many cycles of refinement. ******************************************************************************* ******************************************************************************* Sorry: Please resolve the R-free flags mismatch. While I'm glad that Phenix is checking to ensure that I haven't goofed and tried to switch test sets, I believe I'm being unjustly accused. Why does phenix.refine think I'm a bad boy? Dale Tronrud

2 5

Re: [phenixbb] Autosol Feedback and questions
by Ralf W. Grosse-Kunstleve 02 Jan '08

02 Jan '08

Hi Partha, > 3. I see that phenix.refine has been used in the internal runs, I have used > phenix.refine earlier. But after playing with the side chains in Coot, when > I tried to use the modified pdb file and resolve.mtz, it complained about > the good old Free_R flag. Is this the MD5 error message? > However, it ran directly in Refmac. Is it a known > problem or maybe I did something stupid? I could do a dry run and change > the read mtz and not cns if that would solve the problem. I'm not sure what's going wrong. To be sure, I'd need a reproducer, or at least an exact description of what happened in which order. > 4. Lastly, is it possible to use multiple processors to run the job? No, sorry. Parallelization is a big, complex project. The Cambridge group has started some work in this direction, but it is still very experimental. Ralf

1 0

Fatal Error: Incomplete libtbx environment!
by Yong-Fu Li 01 Jan '08

01 Jan '08

Hi, I just installed Phenix 1.3b, however got this error message when I tried to run phenix. ******************************************* Fatal Error: Incomplete libtbx environment! ******************************************* Please re-run the libtbx/configure.py command. My system is: 2.6.23.8-34.fc7 i686 Here is what I did: 1) downloaded phenix-installer-1.3b-rc6-intel-linux-2.6.tar 2) tar -xvf ... 3) In directory: phenix-installer-1.3b/, execute ./install 4) moved phenix-1.3b-rc6/ from /usr/local to /usr/local/progs where all of my programs dwell 5) source phenix_env in: /usr/local/progs/Phenix/phenix-1.3b-rc6 6) then run: ./phenix, and got the above message 7) as root go to /libtbx, chmod +x configure.py, and ./configure.py (I don't know about python, and my Python is 2.5), it hangs there for very long (>10 min) with another error: ./configure.py: line 3: syntax error near unexpected token `(' ./configure.py: line 3: `def run():' I checked the bb for help but didn't find any useful info (not finished reading all the messages). I wonder whether someone could help! Thanks and happy new year! Yongfu

3 2

heavy atom sites in autobuild
by Bryan W. Lepore 29 Dec '07

29 Dec '07

i'm confused about treatment of heavy atom sites in autobuild. couple questions : 1. since heavy atom sites can be treated as single atoms, should phenix.autobuild simply refine the positions within a protein model? i.e. heavy atom sites should not need to be treated as ligands, with a .cif -- right? 2. if i want autobuild to build around the heavy atom site, can i just use input_pdb_file=heavy.pdb? input_lig_file_list= is not working. -bryan

2 1

Se SAD data to include Sulphurs?
by Partha Chakrabarti 28 Dec '07

28 Dec '07

Hiya, I have a SAD dataset collected at 0.979A to very good completeness and redundancy, upto 2.1A. Two molecules in AU, each containing 2 Se and the solvent content is 40%. The Signal to noise is more than 1 upto 2.1A , however solve resolve and phaser did not work. I am not an expert but what is getting somewhere is if I use SHELEX (or hyss) to find the sites, pick the best 3 of them, use MLPHARE or so to refine and Addsolve to find the other Se. However, looks like the fourth Se is less ordered. Now, the SHELEX file also finds several others which I guess are Sulphurs. I can see helix like density in the map after Addsolve (& resolve) or SHELEXE but have not been able to place any aromatic residue yet. I guess one problem is lack of proper NCS and low solvent content. Could someone point me to a method in which I can improve the map by including the Sulphurs? For example, using the already found Se as seeds? I am trying the autosol option anyway. Cheers, Partha

2 1

Re: [phenixbb] How do I gather the pieces after AutoBuild?
by Thomas C. Terwilliger 27 Dec '07

27 Dec '07

Hi Dale, If you run AutoBuild with "rebuild_in_place=Yes" then it will keep the pieces that you have, try to rebuild them (in nearby locations), and not reassemble the molecule. Rebuilding in place is supposed to be a way to finish off your structure, and that's why it doesn't move it around. In your case, you are rebuilding in place after Phaser molecular replacement. Usually Phaser will make a compact molecule during MR, so this should not normally be a problem. I gather that in this case it didn't do so, however. With rebuild_in_place=No then AutoBuild should try and make a compact molecule. If you have NCS then it will try to make a compact molecule with NCS. All the best, Tom T > Hi all, > > I have finished my Autobuild but the resulting model has some residues > that are scattered in distant asymmetric units. Coot shows their symmetry > images where they belong, next to the rest of the protein. I could > rebuild these residues by hand in the right place, or collecte together > all the symmetry operators and write a script to gather them, but being > lazy would like a more automated solution. Surely this happens to > other people and there is a tool that solves this problem. I've read > a bunch of the web pages for AutoBuild but didn't find a solution there. > > My AutoBuild command was > > phenix.autobuild model=AutoMR_run_4_/MR.1-protein.pdb data=1M50-2.mtz \ > map_file=AutoMR_run_4_/MR.MAP_COEFFS.1.mtz \ > seq_file=../fmo-ct.pir \ > resolution=2.2 dmax=20 refinement_resolution=2.2 \ > cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif > \ > input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \ > rebuild_in_place=Yes > > Shouldn't AutoBuild build a compact model by default? > > Dale Tronrud > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

2 1

How do I gather the pieces after AutoBuild?
by Dale Tronrud 23 Dec '07

23 Dec '07

Hi all, I have finished my Autobuild but the resulting model has some residues that are scattered in distant asymmetric units. Coot shows their symmetry images where they belong, next to the rest of the protein. I could rebuild these residues by hand in the right place, or collecte together all the symmetry operators and write a script to gather them, but being lazy would like a more automated solution. Surely this happens to other people and there is a tool that solves this problem. I've read a bunch of the web pages for AutoBuild but didn't find a solution there. My AutoBuild command was phenix.autobuild model=AutoMR_run_4_/MR.1-protein.pdb data=1M50-2.mtz \ map_file=AutoMR_run_4_/MR.MAP_COEFFS.1.mtz \ seq_file=../fmo-ct.pir \ resolution=2.2 dmax=20 refinement_resolution=2.2 \ cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif \ input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \ rebuild_in_place=Yes Shouldn't AutoBuild build a compact model by default? Dale Tronrud

1 0