- phenixbb - phenix-online.org

Optimizing the Geometry Weight for a 2.76 A structure
by Sam Stampfer 02 Apr '10

02 Apr '10

Hi, I'm refining a 2.76 A structure and need help optimizing the refinement weight on geometry. When I refine at the default refinement weight (wxc = 0.5), phenix seems to generate a much poorer structure (both geometrically AND by Rfree value) relative to lower wxc values which put a stronger weight on geometry. I am trying to pick the best structure to use for my next round of rebuilding. The R-stats and condensed molprobity stats are listed below (at the end of this email). I have a few questions regarding this structure and those stats: 1. What is the relevance of having a LOW difference between Rfree and Rwork? My structure seems to have a higher than expected Rwork value relative to Rfree (aren't they supposed to differ by 0.05 or so, instead of the 0.03 observed in my structure?) Additionally, as I refine at lower wxc values (more weight on geometry) I get an increased Rwork value with an equal or decreased Rfree (relative to the refinement at a higher wxc value). Does that mean my structure is better or worse? 2. How can I judge the output from my refinement? I have looked at Rwork, Rfree, and the molprobity clashscore and overall score values. I included them below, at the end of this email. How do I tell which the best refinement is? Which one would you suggest? I thought the best was wxc = 0.1 since the R-work and Rfree aren't changed much from the start values but the geometry is far better. 3. How do I optimize the weight on geometry in refinement? My PI said that phenix can do it but not for twinned structures (my structure is twinned). Can the new version of phenix do weight optimization for twinned structures? How? If not, what's the best way for me to do it manually? As always, thanks immensely for all your help! -Sam All have the same values for: Start R-work = 0.2002, R-free = 0.2376 *wxc = 0.01 *Final R-work = 0.2104, R-free = 0.2378 Molprobity Clashscore: 19.46 Molprobity Score: 2.29 *wxc = 0.05 *Final R-work = 0.2049, R-free = 0.2377 Molprobity Clashscore: 20.96 Molprobity Score: 2.38 *wxc = 0.1 *Final R-work = 0.2010, R-free = 0.2388 Molprobity Clashscore: 23.50 Molprobity Score: 2.54 *wxc = 0.2 *Final R-work = 0.1969, R-free = 0.2399 Molprobity Clashscore: 27.15 Molprobity Score: 2.79 *wxc = 0.3 *Final R-work = 0.1945, R-free = 0.2411 Molprobity Clashscore: 30.76 Molprobity Score: 2.97 *wxc = 0.4 *Final R-work = 0.1930, R-free = 0.2420 Molprobity Clashscore: 34.54 Molprobity Score: 3.11 *wxc = default (0.5) *Final R-work = 0.1918, R-free = 0.2429 Molprobity Clashscore: 37.73 Molprobity Score: 3.22

6 7

Re: [phenixbb] Optimizing the Geometry Weight for a 2.76 A structure
by det102＠uoxray.uoregon.edu 02 Apr '10

02 Apr '10

Dear Phil, I don't have access to vol 277 of Met Enz here, which is sad since I wrote a chapter in the thing, so I can't comment on Axel's exact words. I agree that the uncertainty in the ability of the free R estimate based on a subset of reflections to predict the mean of the free R calculated from all possible test sets of that size is proportional to 1/N. My point is that the pdf of the difference of two random variables is not the same as the pdf of either of them. You have to know the coupling between them to decide if the difference between them has greater or less precision than the individual variable. For example, let's assume two measurements with a precision of 1% but the difference in the two measurements is 0.5%. This small difference can be significant if the causes of the uncertainties are systematic. The "errors" would cancel out. I believe the fluctuations in free R estimate due to the small size of the test set are due to the particular indices in the test set and therefore mainly systematic. The intensities of some reflections may have been measured better than others and your test set may happen to be more enriched with those, resulting is a slightly lower free R estimate. Since the test set is always the same during refinement the benefit of this enrichment (or detriment if you were unlucky) will be subtracted out when you compare the two free R estimates during your optimization. I expect the difference between two free R estimates (using the same test set) will be a more precise indicator of the true change in free R than either estimate is in predicting the free R itself. Dale Phil Jeffrey wrote: > Although I am totally unclear why the form of the equation, which is > just counting/Poisson statistics, doesn't also apply to the uncertainty > of calculating the average percentage deviation over a test set of size > N. For example a test set of N=1000 could be regarded as 100 different > test sets of size N=10, and I think it's likely that the distribution of > R-free for these 100 mini test sets would be Poisson in form centered > around the R-free for the superset N=1000. > > So, since the change in |Fo-Fc| for each reflection doesn't simply scale > with wxc in structure refinement nor does it inevitably decrease for > every reflection on structure improvement, the change in R-free for any > given change in structure should be related to N in the form of the > equation given, so does reflect the s.d. of R-free as an estimate for > structure improvement. > > No ? > > If not, then I misinterpreted what Brunger mean on p.394 of his 1997 Met > Enz paper because that's certainly what it read like. > > Phil > > det102(a)uoxray.uoregon.edu wrote: >> >> That uncertainty is not quite the same thing. What you describe >> is the uncertainty in the free R due to the small sampling size of >> the test set. It is the spread of free R's obtained when different >> test sets are chosen for the same project and circumstances, and is >> useful when comparing free R's calculated using different test sets, >> or, heaven forbid, trying to compare free R's from different crystals.

1 0

map grid size
by Sean Gay 02 Apr '10

02 Apr '10

Does anyone know if there is a way to increase the map sampling rate for Phenix fofc and 2fofc maps? I want to make a figure for publication in PyMOL and the map_double command helps a bit, but i'd still like more points on the map grids. Sean Sean C. Gay, PhD Postdoctoral Scholar Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego 9500 Gilman Dr. #0703 La Jolla, CA 92093 Tel. (858)822-7804 Fax. (858)246-0089 Email. scgay(a)ucsd.edu

2 1

Double stranded DNA restraints?
by Rajagopalan, Senapathy 02 Apr '10

02 Apr '10

Hi Everyone, Is there a way to force phenix (autobuild) into building a contiguous double stranded DNA. Currently, when I am solving a protein-DNA complex using SAD data: 1) its not recognizing that DNA needs to be double stranded, so it is fitting one of the strands correctly (at least part of it), but the other strand is in the protein density region. 2) It breaks down each of the strand. So it is not fitting as a contiguous 30 mer but instead a 10 mer, two 6 mers and a 8 mer. Thanks Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five 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.

1 0

Secondary structure restraints for nucleic acids
by Peter Grey 02 Apr '10

02 Apr '10

Dear developers, Does the new mechanism of secondary structure restraints apply to nucleic acids as well ? Are the average bond distances similar and does DSSP works well with RNA/DNA ? Thank you in advance for clarifying this issue, Peter.

2 2

Installation problem
by Tatsuya Kaminishi 02 Apr '10

02 Apr '10

Dear Phenix BB When I tried to install the latest binary version (1.6.1), the "install" script always stopped and dumped an error message as follows: ----- /software/PHENIX/phenix-installer-1.6.1-357/bin/install-from-binary: line 347: 10964 Floating point exception$PHENIX_BUILD/base/bin/python $PHENIX_LOC/cctbx_project/libtbx/configure.py -- current_working_directory="$PHENIX_BUILD" $PHENIX_COMPONENTS >> $PHENIX_LOG/binary.log 2>&1 Error configuring: see /software/PHENIX/phenix-installer-1.6.1-357/ build-binary/intel-linux-2.6-x86_64/lupus/log/binary.log for details ----- And this "binary.log" file looks like this; ========== . . After many lines... . ./reduce/comment_out_carboxylate_H_v2.3.pl ./reduce/Makefile ./reduce/libtbx_refresh.py ========== This never happened when I installed version 1.6-289. Could anybody out there tell me how I can get around this? Or anything important is missing? The system I'm using is: Linux crux 2.6.16.60-0.27-smp #1 SMP Mon Jul 28 12:55:32 UTC 2008 x86_64 x86_64 x86_64 GNU/Linux SUSE Linux Enterprise Desktop 10 (x86_64) VERSION = 10 PATCHLEVEL = 2 Thank you very much for your help in advance! Best regards, kami Tatsuya KAMINISHI, Ph.D. Fucini Laboratory Institute for Organic Chemistry and Chemical Biology Johann Wolfgang Goethe University Max-von-Laue-Strasse 7, N160/B413 D-60438 Frankfurt am Main, Germany Tel: +49 69 798-29165 Fax: +49 69 798-29268 Web: http://user.uni-frankfurt.de/~joharms/akfucini/

2 1

Restraints on dihedrals in phenix.refine
by Gregers Rom Andersen 02 Apr '10

02 Apr '10

hi phenix-bb in the standard phenix.refine scripts there are options for adding user defined restraints on bonds and angles, but not on dihedrals. Is this currently possible in phenix.refine? One application would be to restrain the phi-psi angles of a low resolution structure to phi-psi angles from a high-res structure of the same protein, an option previously made possible for xplor in the USF program XPLO2D gregers Gregers Rom Andersen Associate professor Department of Molecular Biology University of Aarhus Gustav Wiedsvej 10C DK8000 Aarhus C phone +45 89425024 fax +45 86123178 www.bioxray.au.dk/gra

3 2

Cadmium missing atoms
by Kristin Sutton 31 Mar '10

31 Mar '10

Hello- I am refining a structure with 2 cadmium ions present. From the extensions menu in coot, I clicked on modeling >> residues with missing atoms, and both Cadmium ions came up in that list. The density surrounding these atoms is also strange, positive density right in the middle of the atom, negative density surrounding the whole atom. How do I make sure these are being refined correctly? Thank you in advance, Kristin ******************************************************************** Kristin A. Sutton Graduate Student University of Buffalo Department of Structural Biology Hauptman-Woodward Medical Research Institute 700 Ellicott Street Buffalo, NY 14203 P: (716)898-8683 F: (716)898-8600 E: ksutton(a)hwi.buffalo.edu

3 3

Phenix version 1.6.1 released
by Paul Adams 30 Mar '10

30 Mar '10

The Phenix developers are pleased to announce that version 1.6.1 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.6.1) are: - Fast automated rotamer fixing in phenix.refine - Use of atomic charge in calculation of scattering factors - New Graphical User Interfaces for phenix.superpose_pdbs, phenix.get_cc_mtz_mtz, phenix.get_cc_mtz_pdb, and phenix.fmodel - Consolidated validation tool in GUI - New map calculation tool, phenix.maps (also used in GUI) - Rapid loading of structures in GUI selection editor - Improved geometry restraints to maintain amino acid rotameric states - Alpha version of secondary structure restraints - Automated secondary structure analysis with KSDSSP (code from UCSF CGL) For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that there is a new publication that should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ PAJimenez(a)lbl.gov ] [ 1-510-486-7963 ] --

1 0

Re: [phenixbb] Citation for xtriage
by Folmer Fredslund 30 Mar '10

30 Mar '10

Dear Mark, On 30 March 2010 19:30, Dr. Mark Mayer <mayerm(a)mail.nih.gov> wrote: > > I'm writing up some results for which we used phenix.xtriage to screen xtals > for twin fraction and would like to know if there is a paper we could/should > cite? > > At the time this work was done we were not using the rest of the phenix > suite for refinement (we are now!). > Going to the phenix FAQS (http://www.phenix-online.org/documentation/faqs.htm#anch2) it would be PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echoo ls, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Or maybe the developers prefer you cite the CCP4 newletters listed at: http://www.phenix-online.org/documentation/xtriage.htm#anch24 Hope this helps, Folmer Fredslund

1 0