- phenixbb - phenix-online.org

workshop abstract
by Tom Terwilliger 20 Feb '08

20 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 14 Feb '08

14 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 14 Feb '08

14 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 12 Feb '08

12 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 09 Feb '08

09 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 08 Feb '08

08 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