- phenixbb - phenix-online.org

on XYZ individual (reciprocal space) refinement
by Dialing Pretty 10 Feb '15

10 Feb '15

Dear All, Will you please tell me the XYZ individual (reciprocal space) refinement is executed by which strategy of the Phnix refinement? By XYZ coordinates, or by Optimize X-ray/ADP weight,or by Optimize X-ray/sterochemistry weight? Dialing

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on my Phenix refinment
by Smith Lee 09 Feb '15

09 Feb '15

Dear All, I have started a Phenix refinement, my strategy including xyz coordinates, real space, individual B-factors, Group B-factors, TLS parameters, Occupancies, optimize X-ray/sterochemistry weight, NCS restraints, and Automatically correct N/Q/H errors. Number of cycles is 3. It is now at the 3' bss stage. But will you please tell me why there is no rsrl stage occurred in the Run Status window (here I mean there is no 1' rsrl stage and 2' rsrl stage) even now it has reached the 3' bss stage? I am looking forward to getting your reply. Smith

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Global metrics for Ramachandran quality beyond %outliers?
by Shane Caldwell 09 Feb '15

09 Feb '15

I'm making a new thread because it's off the topic, but I have a question in response to this point <http://phenix-online.org/pipermail/phenixbb/2015-February/021691.html>: > [Doggy structure improved, as shown by how] The Ramachandran plot tightened This is interesting to me - other than eyeballing the plot, are there any quantitative metrics of Ramachandran distribution quality? At low-res or when refining a bunch of structures side-by-side it could be an additional indicator of quality of the model, without requiring having to inspect the plot. Of course manual inspection is always important in the end, but in early stages a global measure of spread could help guide refinement. I've seen %outliers used for this purpose, but that ignores that while a residue can be "allowed" it can still be far from a statistically likely conformation. From what I've seen, some users only consult Ramachandran to tweak residues until they pop into the "allowed" regions and stop there, which isn't the same as globally improving the geometry. Interested to hear thoughts (or it it's already in use, pointing me in the right direction!), Shane Caldwell McGill University On Thu, Feb 5, 2015 at 5:06 AM, Andreas Förster <docandreas(a)gmail.com> wrote: > Dear Almudena, > > I promise not to make a habit of advertising other programs on the Phenix > mailing list, but just once I would like to encourage you (and the > community) to try all the tools at your disposal. > > Different refinement programs have different strength and weaknesses. > Secondary-structure restraints in Phenix are great for low-resolution data, > but so is jelly-body refinement in Refmac. A dodgy 3.2 Å structure I'm > currently working on was improved dramatically by Buster-TNT. The > Ramachandran plot tightened, and R free plunged by four percentage points. > > > Andreas > > > > On 05/02/2015 10:44, Almudena Ponce Salvatierra wrote: > >> Dear all, >> >> I am refining my structure (data at 3 A), with a model that is complete. >> However the Rs values are: R work= 0.25 and Rfree= 0.32. I have read >> "Improved target weight optimization in phenix.refine" (In the >> computational crystallographic newsletter 2011) and what I understand is >> that just by marking the boxes "improve xray/stereochemistry weight" and >> "improve xray/adp weight" it should work... giving me the best possible >> Rfree. >> >> I'm refining individual coordinates, occupancies, b-factors (isotropic >> for all atoms), TLS, and using secondary structure restraints, automatic >> ligand linking and experimental phases restraints. Also, I chose this >> strategy because I have finished building the structure and according to >> some of the suggestions in "towards automated crystallographic structure >> refinement with phenix.refine". >> >> I am actually quite confused and don't know what to think... is it a >> matter of the weights? is it only that this is as good as it gets? >> >> Any suggestions and comments are welcome. >> >> Thanks a lot in advance, >> >> Best, >> >> Almudena >> -- >> Almudena Ponce-Salvatierra >> Macromolecular crystallography and Nucleic acid chemistry >> Max Planck Institute for Biophysical Chemistry >> Am Fassberg 11 37077 Göttingen >> Germany >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

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Scientist BioMAX
by Marjolein Thunnissen 07 Feb '15

07 Feb '15

Beamline manager position open for BioMAX Beamline The MAX IV Laboratory, a part of Lund University, has operated successfully for more than 25 years and is currently building the new MAX IV synchrotron facility in Lund. More than 900 scientists from Sweden and the rest of the world are coming to the MAX IV Laboratory every year to use the x-rays produced by our electron accelerators. They do research in areas such as materials science, structural biology, chemistry, and nanotechnology. 170 people are currently employed at the MAX IV Laboratory. The MAX IV facility, the largest and most ambitious Swedish investment in research infrastructure, will be the brightest source of x-rays worldwide and will replace the existing laboratory, which today consists of the storage rings MAX I, II and III. The new MAX IV facility will become operational in June 2016. One of the first beamline at MAX IV to come into operation will be the macromolecular crystallography (MX) beamline BioMAX. BioMAX will use the unique properties of the MAX IV 3 GeV ring to become a world leading MX beamline with a high degree of automation, microfocus capability, highly parallel beam suitable for large molecular assemblies, high flux, high level of software support and a user friendly environment. We are now looking for a beamline manager for the BioMAX beamline. Link to full posting: http://www.lu.se/lediga-anstallningar-available-jobs?x=0&Dnr=654959&Type=E Job Location: MAX IV-Laboratory, Lund, Sweden Job Title / Reference: Scientist BioMAX / Ref: PEPA 2015/9 Application deadline: Wednesday, February 18, 2015 For further information please contact: Tomas Lundqvist<mailto:[email protected]>, Life Science Director | +46708467688 best regards Marjolein [cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC] Marjolein Thunnissen Science Coordinator Structural Biology MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se<http://www.maxlab.lu.se/> [cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC] Marjolein Thunnissen Science Coordinator Structural Biology MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se<http://www.maxlab.lu.se/>

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allowable completeness limit for the highest resolution shell
by Tarek DawoD 06 Feb '15

06 Feb '15

Dear ALL i would like to ask in general if there is a suggested certain completeness cutoff for the higher resolution shell. for example; the following are the values for the 4 higher resolution shells Shell Lower Upper Average Average Norm. Linear Square limit Angstrom I error stat. Chi**2 R-fac R-fac Rmeas Rpim CC1/2 CC* completeness 1.53 1.50 2.5 1.2 1.2 0.706 0.680 0.596 0.855 0.510 0.547 0.841 73.6 1.50 1.47 2.3 1.1 1.0 0.745 0.742 0.629 0.967 0.613 0.468 0.798 55.3 1.47 1.44 2.0 1.0 1.0 0.725 0.775 0.644 0.000 0.694 0.395 0.752 52.4 1.44 1.41 1.9 0.8 0.8 0.689 0.946 0.681 0.000 0.883 0.371 0.736 33.9 All reflections 44.8 2.5 2.3 0.638 0.044 0.029 0.052 0.028 my question in other word if all statistics for the highest resolution shell are reasonable, good I/sigma, R-fac, ........, CC1/2, ..etc but the completeness is just say 20 or 30, what is allowable completeness limit for the highest resolution shell, 70, 80 or 90??? regardsTK_Dawod

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refinement with anomalous data
by Guangyu Zhu 06 Feb '15

06 Feb '15

Hi, all, I have a question for refinement. I have a data set for refinement at 3.8A (outshell I/sigma ~1.0). When I processed the data, I kept anomalous data I+/I-. Because at that time I think I might have anomalous signal. But later I found that the protein coordinated with wrong metal, so I don’t really have anomalous scatters. I have good model from high resolution data. When I refined the structure, I found that refined against I+/I- give lower R/Rfree (23.0%/27.0%) than against Imean (25.1%/28.3%). When I used I+/I-, I knew I doubled reflections/parameters ratio. I also let Phenix both X-ray stereochemistry/ADP weight. The refined models have similar geometry. So should I use I+/I- for refinement since it gives lower R factor? Guangyu Zhu

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Fwd: [ccp4bb] Absence of contact between layers in a crystal
by Folmer Fredslund 06 Feb '15

06 Feb '15

Hi all, As you might have noticed, there is a discussion going on about the fraudulent 2hr0 pdb deposition on the CCP4BB Searching for 2hr0 I came across http://www.phenix-online.org/documentation/reference/cif_as_mtz.html where 2hr0 is used as an example. Might I suggest that this is changed in the documentation? Best regards, Folmer Fredslund ---------- Forwarded message ---------- From: Kerff Fred <fkerff(a)ulg.ac.be> Date: 2015-02-06 11:58 GMT+01:00 Subject: [ccp4bb] Absence of contact between layers in a crystal To: CCP4BB(a)jiscmail.ac.uk Hello, Looking at structure 2HR0 ("The structure of complement C3b provides insights into complement activation and regulation. »,Abdul Ajees, A., Gunasekaran, K., Volanakis, J.E., Narayana, S.V., Kotwal, G.J., Krishna Murthy, H.M.; (2006) Nature 444: 221-225), I noticed the absence of contacts between layers in the crystal. Is it something that has already been observed in other crystals? Best regards, Fred ----- Frédéric Kerff Chercheur qualifié F.R.S.-FNRS Cristallographie des protéines Centre d'Ingénierie des Protéines Université de Liège 17, Allée du 6 Août - Bat B5a 4000 Liège (Belgium) Tel.: +32 (0)4 3663620 Fax: +32 (0)4 3663772 > Le 6 févr. 2015 à 10:12, Tim Gruene <tg(a)SHELX.UNI-AC.GWDG.DE> a écrit : > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Smith, > > The sca file most likely does not contain flags. pointless can read > the sca file, standardise it to ccp4 standards and freerflag marks > random reflections. You should use the maximum of 500 unique > reflections or 5% of the unique reflections, whichever is larger. > > Best, > Tim > > On 02/06/2015 09:49 AM, Smith Lee wrote: >> Dear All, I have a sca file. Will you please tell me by which >> software or how I can know whether the sca file contains R-free >> tags? If not, by which software or how I can add the R-free tags? >> And how much of the reflections I add the R-free tags? I am looking >> forward to getting your reply. Smith >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > > iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi > j0JFZac4kAh8twpov71MG84= > =XN57 > -----END PGP SIGNATURE----- -- Folmer Fredslund

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Phenix refine - R free does not decrease
by Almudena Ponce Salvatierra 06 Feb '15

06 Feb '15

Dear all, I am refining my structure (data at 3 A), with a model that is complete. However the Rs values are: R work= 0.25 and Rfree= 0.32. I have read "Improved target weight optimization in phenix.refine" (In the computational crystallographic newsletter 2011) and what I understand is that just by marking the boxes "improve xray/stereochemistry weight" and "improve xray/adp weight" it should work... giving me the best possible Rfree. I'm refining individual coordinates, occupancies, b-factors (isotropic for all atoms), TLS, and using secondary structure restraints, automatic ligand linking and experimental phases restraints. Also, I chose this strategy because I have finished building the structure and according to some of the suggestions in "towards automated crystallographic structure refinement with phenix.refine". I am actually quite confused and don't know what to think... is it a matter of the weights? is it only that this is as good as it gets? Any suggestions and comments are welcome. Thanks a lot in advance, Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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Strange behaviour of phenix.maps fill_missing_f_obs
by Tristan Croll 06 Feb '15

06 Feb '15

Hi, I'm working on a package that makes scripted calls to phenix.refine to generate a series of ccp4 formatted maps, and have run into an odd problem. Using the attached parameter file I get a series of perfectly normal-looking maps, except in the case of the filled 2mFo-DFc map (test-3_2mFo-DFc_fill.ccp4 - the second-last map generated). This comes out as a series of disconnected blobs (it looks rather like a mFo-DFc map, but it doesn't match the actual mFo-DFc map). When I take the resulting .mtz file and generate the filled map in Coot (with or without omission of Rfree flags), on the other hand, it seems to come out fine. There are no error messages in the log, but I suspect the default method to fill in the missing F_obs may be returning only the missing F_obs? I've attached a small example image. Red wireframe is the 2mFo-DFc unfilled map at 1 sigma; green translucent is the 2mFo-DFc filled map at 1 sigma; yellow is the mFo-DFc map at 2 sigma. The test structure I'm using is nothing special: 3WSY, picked more-or-less at random off the protein data bank. Phenix version is 1.9.1692, installed in Fedora 21. Have I done something wrong that I'm just not seeing, or is there a bug here? Thanks, Tristan

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off-topic: Faculty position at all levels in structural biology at Stony Brook University, New York
by Markus Seeliger 05 Feb '15

05 Feb '15

We are recruiting for the above position. More details and the application can be found at https://academicjobsonline.org/ajo/jobs/5289 Stony Brook University Department of Pharmacological Sciences *Tenure-Track Structural Biology / Imaging Faculty Position in Conjunction with the Interdisciplinary Biomolecular Imaging Cluster Hiring Initiative* The Department of Pharmacological Sciences ( http://www.pharm.stonybrook.edu/faculty_research/overview) at Stony Brook University seeks applications for a tenure-track faculty position at the level of Assistant, Associate, or Full Professor. Candidates must have an M.D. and/or Ph.D., at least two years of postgraduate research experience, and an outstanding record of research accomplishment. This search is intended to recruit investigators with translational research programs that make use of *NMR, Cryo-EM, or positron emission tomography (PET) coupled with radiotracer synthesis approaches* to pursue fundamental questions relevant to health-connected fields such as cancer, neuroscience, metabolism, and infectious disease. Senior candidates should also have a record of success with extramural funding and training of students and/or fellows. Applicants must be eligible for a faculty appointment in accordance with the criteria established by the School of Medicine (Criteria for Appointment, Promotion and Tenure.) The Department has pre-doctoral and MSTP training grants, a broad infrastructure for research investigation, and newly renovated lab space housing structural biologists with expertise in NMR and x-ray crystallography. Additional structural biologists and PET imagers are found in the Departments of Biochemistry, Physiology, Chemistry, and Microbiology. With the on-going NYSUNY 2020 Challenge Grant awarded to the University and the recent and largest gift ever to public higher education in the State of New York, Stony Brook University is embarking on a transformational expansion of the biomedical research enterprise. Diverse opportunities for collaborative research on campus include the Cancer Center, the Laufer Center for Physical and Quantitative Biology, the Center for Structural Biology, the Institute for Chemical Biology and Drug Discovery, and the interactive Computer Science and Applied Mathematics Departments. Imaging biological molecules is key to understanding their function, providing a starting point for rational drug design and protein engineering. Stony Brook University is becoming a leader in biomolecular imaging through its newly-upgraded high-field NMR facilities including Bruker 700MHz and 850 MHz instruments with cryogenic probes, a strong program in computational structural and physical biology, world-class computational resources, facilities for radiotracer synthesis and human imaging, and proximity to the new third-generation synchrotron facility at Brookhaven National Lab (NSLS-II). The Biomolecular Imaging Cluster has already recruited junior faculty with expertise in super-resolution microscopy and x-ray crystallography. Stony Brook University, home to many highly-ranked graduate research programs, is located 60 miles from New York City on Long Island's scenic North Shore. Our 1,100-acre campus has more than 24,000 undergraduate, graduate, and doctoral students and 13,500 faculty and staff. The University is a member of the prestigious Association of American Universities and co-manager of the nearby Brookhaven National Laboratory, a multidisciplinary research laboratory supporting world-class scientific programs utilizing state-of-the-art facilities. Stony Brook University is also located close to the Cold Spring Harbor Laboratory with which it interacts through graduate program training and faculty collaborations. To apply, use Academic Jobs Online ( https://academicjobsonline.org/ajo/jobs/5289) to submit a State employment application, a complete curriculum vitae including publications, and a 3-page proposed research plan of current and future research, and have three letters of recommendation submitted through the AJO site. The cover letter should indicate whether the applicant wishes to be considered for appointment at the Assistant, Associate, or Full Professor level. Applicants at the Associate or Full Professor level should add a summary of past and current research funding and administrative and teaching experiences. Electronic submission through AJO is required. Questions should be addressed to Ms. Lynda Perdomo-Ayala, Department Administrator ( lynda.perdomo-ayala(a)stonybrook.edu). 631-444-3050 For a full position description, visit www.stonybrook.edu/jobs (Ref. F-9387/14/12.) Stony Brook University is an Affirmative Action, Equal Opportunity Educator and Employer.

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generating xplor map of specific size
by Scott Horowitz 03 Feb '15

03 Feb '15

Hi all, Sorry for yet another map question: what I'd like to do is be able to generate xplor maps with an explicitly defined size and shape from the command line using phenix. Just choosing a buffer around a selection will result in slightly different sizes for different PDB files, which I'd like to avoid. In my comparisons, having exactly the same dimensions and centering for maps I'm calculating from multiple slightly different variants would be very helpful. Is there a way to do this? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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serial MR / refinement
by Eike Schulz 03 Feb '15

03 Feb '15

Dear all, I am looking for a way to automate molecular replacement and refinement runs. >From ligand / fragment screening trials we have many datasets of the same protein with various resolutions (2.8 – 1.2Å). The apo-structure is known and well refined. The cell constants are fairly similar but not in all cases identical, hence I would prefer a MR run prior to the refinement. I am sure this can somehow be realized with some shell-script but maybe there is some more sophisticated way of realising this? I would also be happy for partial solutions to the problem. Best regards Eike

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Young scientist travel awards for Intl Conf. on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology"
by Terwilliger, Thomas Charles 02 Feb '15

02 Feb '15

2-Feb-2015 Dear Colleagues, We are pleased to announce the availability of young scientist travel fellowships to the International Conference on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology", which will be held on the campus of the Weizmann Institute of Science in Rehovot, Israel June 7-11, 2015. This conference is intended to foster international collaboration and to provide an overview for the most recent developments in Structural Biology and Structural Genomics and future impacts on biology, medicine and disease. Web site: http://www.weizmann.ac.il/conferences/ICSG2015 Poster: https://www.dropbox.com/s/i1s3hsg7a0chqi2/ICSG2015_Poster.pdf?dl=0 There are two types of young scientist travel support available (deadlines are both March 31, 2015): Young scientist travel support of up to $1,000 US will be made available to graduate students and post-doctoral researchers to attend ICSG2015. A total of 5 International Structural Genomics Organization (ISGO) - NIH Protein Structure Initiative (PSI) Student Travel Fellowships have kindly been provided by the ISGO and the NIH PSI. Fellowships of €500 for students from Instruct countries will be awarded to attend the pre-conference workshop “Technical and Analytical Approaches to the Translation of Deep Sequencing Data into Three-Dimensions” (7-June-2014 09:00-12:00) and to stay on and participate in the full conference. A total of 8 Fellowships have kindly been provided by Instruct (https://www.structuralbiology.eu). To apply for a student travel fellowship please see http://www.weizmann.ac.il/conferences/ICSG2015/young-scientists-travel-supp… . The International Conference on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology” conference The scientific topics to be covered in ICSG 2015 (see http://www.weizmann.ac.il/conferences/ICSG2015) include: · Deep sequencing for modeling and refinement of macromolecular structures · Membrane protein structure and function using complementary methods · Technological advances in XFEL, Cryo-EM, NMR, SAXS, MS, MX and macromolecular complexes · Combining low and high resolution data and modeling for structural biology · Synergistic use of 3D structures and deep sequencing to realize personalized medicine · Protein design and deep sequencing · Cancer, antibiotic resistance and drug discovery In order to widen the opportunities for younger researchers, we have organized satellite workshops before ICSG 2015 (during the day on June 7, 2015). These include: · Cryo-EM developments for structural biology [Sponsored by FEI] · Approaches to the translation of deep sequencing data into three-dimensions [Sponsored by Instruct] · PHENIX: Automated determination of molecular structures [Tom Terwilliger & Pavel Afonine] · HKL3000: From X-ray diffraction images to structure determination in minutes [Wladek Minor] · Protein expression and characterization workshop [Tamar Unger & Yoav Peleg] · Proteopedia: A Scientific Wiki Bridging the Rift Between 3D Structure & Function [Jaime Prilusky & Joel L. Sussman] Five oral presentations will be chosen from the posters, and six poster prizes will be awarded, so be sure to submit your abstracts by April 15, 2015! Speakers include: Arie Admon (Haifa) Lucia Banci (Florence) Pamela J. Bjorkman (Pasadena) Samir K. Brahmachari (Delhi) Susan Buchanan (Bethesda) Martin Caffrey (Dublin) Mark Gerstein (New Haven) Wayne Hendrickson (New York) Yvonne Jones (Oxford) Roger Kornberg (Stanford) Luhua Lai (Beijing) Michael Levitt (Stanford) Michal Linial (Jerusalem) Abraham Minsky (Rehovot) John Moult (Rockville) Nathan Nelson (Tel Aviv) Stefan Raunser (Dortmund) Monica Roth (Piscataway) Dinakar M. Salunke (Gurgaon) Eran Segal (Rehovot) Philip Selenko (Berlin) Sachdev Sidhu (Toronto) Rotem Sorek (Rehovot) Jan Steyaert (Brussels) Shamil Sunyaev (Boston) Dan Tawfik (Rehovot) Janet Thornton (Hinxton) The FEBS National Lecturer Gunnar von Heijne (Stockholm) Soichi Wakatsuki (Stanford) Shigeyuki Yokoyama (Yokohama) Ada Yonath (Rehovot) Mingjie Zhang (Hong Kong) We are looking forward to welcoming you to the Weizmann Institute in the June of 2015! Sincerely yours, ICSG 2015 Local Organizing Committee Joel L. Sussman, Gideon Schreiber, Tamar Unger and Israel Silman, Weizmann Institute ICSG 2015 International Organizing Committee Cheryl Arrowsmith, (Structural Genomics Consortium, Toronto) Lucia Banci, (University of Florence, Florence) Jacqui Beckmann, (Swiss Institute of Bioinformatics, Lausanne) Mark Gerstein, (Yale University, New Haven) Yvonne Jones, (University of Oxford, Oxford) ------------------------------------------------------------------------- Prof. Joel L. Sussman www.weizmann.ac.il/~joel<http://www.weizmann.ac.il/~joel> Department of Structural Biology tel: +972 (8) 934 4531 www.weizmann.ac.il/ISPC<http://www.weizmann.ac.il/ISPC> Weizmann Institute of Science fax: +972 (8) 934 6312 www.proteopedia.org<http://www.proteopedia.org> Rehovot 76100 ISRAEL www.weizmann.ac.il/conferences/ICSG2015<http://www.weizmann.ac.il/conferences/ICSG2015> -------------------------------------------------------------------------

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Output file of the Phenix refine
by Smith Liu 02 Feb '15

02 Feb '15

Dear All, Will you please tell me which Phenix refine output file contains the information on my input files, my strategies and my parameters for the refinement? Smith

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Question related to Phenix refinement
by Smith Lee 02 Feb '15

02 Feb '15

Dear All, Which strategy or parameter input can be used to reduce the rotamer outliers? Which strategy or parameter input can be used to reduce the bond outliers? For all the Phenix refine strategies, can you sequence it from rough refinement to fine refinement in order? I am looking forward to getting your reply. Smith

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Rwork and Rfree
by Dialing Pretty 31 Jan '15

31 Jan '15

Dear All, After a Phenix refinement (for crystal 2.5A), my Rwork is about 0.19, and my Rfree is about 0.26. Is the gap between Rwork and Rfree too karge? If too large, why it is too large and how to avoid it? I am looking forward to getting your reply. Dialing

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Re: [phenixbb] making coarse maps
by Terwilliger, Thomas Charles 30 Jan '15

30 Jan '15

Hi Scott, You can use the reflection file converter in the GUI to write out map coefficients with any resolution cutoff that you like. That may be the easiest. Alternatively you can take your refined model and use phenix.maps to calculate a map at any resolution that you like without further refinement. You might also consider just adjusting the sharpening on your map which will have something of the same effect as cutting the resolution. All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Scott Horowitz [horowsah(a)umich.edu] Sent: Friday, January 30, 2015 6:09 AM To: PHENIX user mailing list Subject: [phenixbb] making course maps Hi all, Although I realize this sounds counterproductive, I'd really like to be able to make a map with grid spacing that is around 3 A, even though I have a ~2 A structure, and I don't want to have to cut data before refinement. However, it seems like the max number I can give to the grid resolution factor is 0.5. Is there a way to break this limit without it crashing? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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making course maps
by Scott Horowitz 30 Jan '15

30 Jan '15

Hi all, Although I realize this sounds counterproductive, I'd really like to be able to make a map with grid spacing that is around 3 A, even though I have a ~2 A structure, and I don't want to have to cut data before refinement. However, it seems like the max number I can give to the grid resolution factor is 0.5. Is there a way to break this limit without it crashing? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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calculating map from pdb
by Scott Horowitz 29 Jan '15

29 Jan '15

Hi all, I was wondering how to quickly back-compute an electron density map from a PDB using phenix from the command line. I'm assuming it's not hard, but I can't find documentation that would lead me to it. Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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question about mmtbx.prepare_pdb_deposition
by Gerwald Jogl 28 Jan '15

28 Jan '15

Hi, How does the sequence file for this tool have to be formatted when there are more than one proteins/sequences in the asu? Does the program match this automatically? Thanks, Gerwald

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Old Phenix jobs
by Mark A Saper 27 Jan '15

27 Jan '15

I was looking at some old Phenix GUI jobs run in Sept 2010 with Phenix version 1.6.4. Can these jobs be opened with the current (dev-1932) GUI ? When I try to restore a refinement job opens, a window opens with the parameters used for the job, but no tab with the results. When I try to restore other jobs, I receive an error when trying to open them: “UnicodeDecodeError : ‘utf8’ codec can’t decode byte 0x81 in position 35: invalid start byte”. Another thing I noticed about some of these jobs was that there are *.libtbx_info files in the phenix/tmp subdirectorty that are >100 Mbytes, even one that is 1.2 Gbytes! Can these files be deleted. I only see such large files for one particular structure. Any info about this would be helpful. Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School 3040 Chemistry Building | saper(a)umich.edu | +1 (734) 764-3353

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R/ R free (overall) and R/Rfree (for highest resolution shell)
by George Devaniranjan 27 Jan '15

27 Jan '15

Hi, I calculated/validated several PDB structures in Phenix.Validation (GUI) The R/R-free (overall) is 0.1271/0.1348 Further down I looked at the R/R-free for the highest resolution shell. Its 0.2538/0.2446 I am curious why the R-free for the *highest resolution shell* seems to be LOWER than R (work). Am I reading the information wrong? PDB: 3QL9 Thank you, George

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Re: [phenixbb] phenixbb Digest, Vol 110, Issue 12
by Kay Diederichs 25 Jan '15

25 Jan '15

Patrick, see my posting at https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;f6735c0c.1501 . The "Advanced Search" interface of the RCSB also lets you search for resolution range and many other criteria. "Text search" won't help you much if you are searching specific numeric values, I guess. best, Kay Am 25.01.15 um 09:21 schrieb phenixbb-request(a)phenix-online.org: > Date: Sat, 24 Jan 2015 09:41:36 -0800 > From: Patrick <patrick.cossins(a)inbox.com> > To: PHENIX list <phenixbb(a)phenix-online.org>, ccp4bb(a)jiscmail.ac.uk > Subject: [phenixbb] extracting PHENIX structures > Message-ID: <5D1147D5283.0000050Apatrick.cossins(a)inbox.com> > Content-Type: text/plain; charset=US-ASCII > > Hi, > > not directly related but I wanted to know how to extract from the PDB all the PHENIX/CCP4 refined structures currently deposited. > > Do I use the "text" search in quarry to get the result or do I use the software? > > I tried it for both but seems to give different results (no's). > > I tried for another refinement package (shelx) and same, different no's > > Using software, and looking for contains 320 > > using text search 130 > > Is there another way to get structure of a certain resolution ? > > Patrick

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extracting PHENIX structures
by Patrick 24 Jan '15

24 Jan '15

Hi, not directly related but I wanted to know how to extract from the PDB all the PHENIX/CCP4 refined structures currently deposited. Do I use the "text" search in quarry to get the result or do I use the software? I tried it for both but seems to give different results (no's). I tried for another refinement package (shelx) and same, different no's Using software, and looking for contains 320 using text search 130 Is there another way to get structure of a certain resolution ? Patrick ____________________________________________________________ Can't remember your password? Do you need a strong and secure password? Use Password manager! It stores your passwords & protects your account. Check it out at http://mysecurelogon.com/password-manager

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Crystallography Workshop in South America - CCP4 / Institut Pasteur de Montevideo 2015
by Alejandro Buschiazzo 24 Jan '15

24 Jan '15

Dear colleagues, We wish to remind you about the upcoming Workshop: Macromolecular Crystallography School "From data processing to structure refinement and beyond", to be held at the Institut Pasteur de Montevideo (Uruguay). Dates: April 6 - 16, 2015 Invited speakers and tutors: Alejandro Buschiazzo, Montevideo, Uruguay Kay Diederichs, Konstanz, Germany Paul Emsley, Cambridge, UK Richard Garrat, São Carlos, Brazil Ronan Keegan, Oxford, UK Eugene Krissinel, Oxford, UK Victor Lamzin, Hamburg, Germany Andrey Lebedev, Oxford, UK Andrew Leslie, Cambridge, UK Garib Murshudov, Cambridge, UK Rob Nicholls, Cambridge, UK Randy Read, Cambridge, UK William Shepard, Paris, France Pavol Skubak, Leiden, the Netherlands Clemens Vonrhein, Cambridge, UK This edition will count with an optional introductory day. A Scientific Satellite Symposium will take place during the course. Sponsored by the Insttitut Pasteur and the Institut Pasteur International Network, this symposium will gather top research scientists from the Pasteur Network, who will discuss about Structural Biology in the study of infectious diseases: Pedro Alzari and Michael Nilges (Inst Pasteur, Paris), Beatriz Guimaraes (Fiocruz, Parana) and Joo Hwan No (Inst Pasteur, Korea), together with several scientists from Inst Pasteur Montevideo. Please find the program of the Workshop and Satellite Symposium, the application form and further contact information, at www.pasteur.edu.uy/mx2015 <http://www.pasteur.edu.uy/mx2015> The site will be updated regularly, stay tuned. We acknowledge the support from the Reseau International des Instituts Pasteur (RIIP); the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the International Union of Crystallography (IUCr); and the Institut Pasteur de Montevideo. Applicants: 24 students will be selected, aiming at advanced PhD, postdocs and young researchers. The Course will provide financial support covering registration fees, and for the case of those students coming from abroad, all local expenses (lodging, per diem and local transportation). Look in the www site <http://www.pasteur.edu.uy/mx2015> for details on application procedures. The application deadline is February 16, 2015. The results will be announced by March 6. Please address further inquiries to: mx2015(a)pasteur.edu.uy <mailto:[email protected]> Organizers: Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom We look forward to welcoming you soon in Montevideo! -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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Problem during refinement
by Almudena Ponce Salvatierra 24 Jan '15

24 Jan '15

Dear all, I have partially rebuilt my model after autosol and now I would like to submit it for refinement to Phenix refine. However when I do so, even though the R factors go down when I have a look at the result, it just looks awful! All the model is placed out of the electron density map, plus the electron density map doesn't look anymore like a 3 A one, but just like sausages. Why is this happening? The truth is I have no idea... What I do is to provide Phenix refine with overall_best_refine_data.mtz (coming from autosol) as phases, x Ray data and x Ray r free data. Additionally, the starting model and the sequence. Any suggestions are more than welcome. Thanks a lot in advance. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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resolve phases/fom
by "Weiergräber, Oliver H." 24 Jan '15

24 Jan '15

Hello, while compiling phasing stats for a manuscript, I came around the following question: Having run autosol (on a SAD dataset) from the command line, where to find the latest density-modified phases (with associated FOMs) _before_ the onset of model building? The PHIM and FOMM columns in the denmod_i.mtz files are obvious candidates - just want to be sure since this particular FOM does not seem to be echoed in the log files, as far as I can see. Best regards Oliver ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Reflection file editor. copying Free set from one to other mtz.
by Tarek DawoD 23 Jan '15

23 Jan '15

Unfortunately i did not find a detailed explanation for how to use reflection file editor (GUI) i just want to know if i am right and i have a questions about how it works as well 1- if i have 2 myfile-data.mtz files (for the same structure but 2 different ligands, one of them 1.9 A and the other 1.6 A) and i want to copy free set from one to the other. so i have in the (ALL Input Arrays) 2 intensity and 2 R-free flag. so what i did is to add in the (output array) one of the intensity which belongs to one and one R flag which belong to other. i was not sure how to use the other output options??? what should i check or uncheck in this particular case??? 2- How this works? suppose i have h k l (6 7 21) has flag 1 in the data.mtz file (the one i used to copy the free set to other mtz), if i will copy this to other mtz (which has no R flag of course), the program will look for (6 7 21) h k l in the other mtz to give it also flag 1. Am i right.??? 3- if i am right in number 2, Suppose the other mtz has no (6 7 21) h k l what will happen? if it is just ignoring it or assign flag 1 for other h k l which did not exist in the first data.mtz.this means it is impossible to get 100% free set similar between say the 2 mtz files in this case. thank you in advance thank you Dr Pavel and Dr Georg for your reply to my previous query TK DawoD

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Solving installation problems on network volumes in Yosemite
by Chris Richardson 23 Jan '15

23 Jan '15

I thought I’d post this in case anyone has a similar problem in the future. It’s taken me a couple of days of frustration to find the solution; maybe I can save someone else some pain. This problem only occurs when trying to install Phenix on an NFS-mounted volume in OS X 10.x, Yosemite. If this doesn’t apply to you (and I might be the only person doing this), you can happily ignore what follows. The problem: In an effort to save us from malware, OS X now adds a ‘quarantine’ attribute to downloaded files. This includes tar and compressed tar files. For most users the quarantine flag only really comes into play if the downloaded file is an application or installer package. When Yosemite untars an archive with the quarantine attribute, it adds the quarantine attribute to every file it extracts from the archive. This doesn’t present a problem if you’re extracting the archive to a local disk, or an AFP-mounted network volume. If you’re extracting the archive to an NFS-mounted network volume, it can’t store the quarantine flag as a resource fork on the file itself. Instead, it creates a ._<filename> file for each extracted file. The Phenix installer doesn’t like having an install tree full of unexpected ._ files. In some cases, such as where generate_henke_cpp.py tries to generate tables from all the files in a directory, it tries to read ._ files as normal files and dies. The solution: The solution is trivial once you know what the problem is. Remove the quarantine attribute from the tar file before extracting its contents. For example: xattr -d com.apple.quarantine phenix-installer-1.9-1692-mac-intel-osx-x86_64.tar.gz Of course, if the Phenix installer could be modified so that it doesn’t die when it finds unexpected ._ files, that would be lovely. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Rfree % calculation
by Tarek DawoD 22 Jan '15

22 Jan '15

Dear ALL when you start you refinment in phenix with ***.sca file, fraction of reflection in test set will be created. under options (bottom) in phenix refine, you could see that fraction of reflection in test set is 0.1 which means 10 %by looking to the PDB header for completely different structures (below) you will find different percentage but always FREE R VALUE TEST SET COUNT is around 3800. so it always take the same 3800 count regardless the number of reflections. when you look in generated mtz file after the refinment, you see under R-free-flags(+) and R-free-flags(-) either 0 or 1. what does 0 or 1 mean? thank you in advance for explaination. TKDawoD ----------------------------------------------------------------------------------------------------REMARK 3 NUMBER OF REFLECTIONS : 47312 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 24389 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT.REMARK 3 R VALUE (WORKING + TEST SET) : 0.1673REMARK 3 R VALUE (WORKING SET) : 0.1636REMARK 3 FREE R VALUE : 0.2084REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.21 REMARK 3 FREE R VALUE TEST SET COUNT : 3882------------------------------------------------------------------------------------------------------REMARK 3 NUMBER OF REFLECTIONS : 107005 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 56251 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT.REMARK 3 R VALUE (WORKING + TEST SET) : 0.1457REMARK 3 R VALUE (WORKING SET) : 0.15.34REMARK 3 FREE R VALUE : 0.1997REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.51 REMARK 3 FREE R VALUE TEST SET COUNT : 3809-----------------------------------------------------------------------------------------------------NUMBER OF REFLECTIONS : 48150 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 25296 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT.REMARK 3 R VALUE (WORKING + TEST SET) : 0.1507REMARK 3 R VALUE (WORKING SET) : 0.1470REMARK 3 FREE R VALUE : 0.1918REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.98 REMARK 3 FREE R VALUE TEST SET COUNT : 3841

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Problems installing Rosetta
by 신인철 20 Jan '15

20 Jan '15

Hi, I am trying to install rosetta on Fedora 21. I downloaded rosetta_bin_linux_2015.02.57538_bundle.tgz and copied the unpacked whole directory under /usr/local/ and rename "rosetta_bin_linux_2015.02.57538" as "rosetta" simply. And I edited .cshrc file like: setenv PHENIX_ROSETTA_PATH "/usr/local/rosetta" setenv ROSETTA3_DB "usr/local/rosetta/main/database" But encountered the following messages: [root@localhost ~]# rosetta.build_phenix_interface nproc=8 False scons: Reading SConscript files ... Running versioning script ... Done. (0.0 seconds) Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: File "/usr/local/rosetta/main/source/SConstruct", line 172: main() File "/usr/local/rosetta/main/source/SConstruct", line 163: SConscript("SConscript", "build") File "/usr/local/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: return method(*args, **kw) File "/usr/local/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: return _SConscript(self.fs, *files, **subst_kw) File "/usr/local/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: exec _file_ in call_stack[-1].globals File "/usr/local/rosetta/main/source/SConscript", line 28: subprocess.check_call(["./update_options.sh"]) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 540: raise CalledProcessError(retcode, cmd) What am I going to do? Please, help!! ------------------------------------------------- Inchul Shin School of Agricultural Biotechnology Seoul National University Seoul, KOREA 151-921 Tel: +82-2-880-4633 Fax: +82-2-873-4950 Mobile: +82-10-6215-2896 Email: ichul96(a)snu.ac.kr<mailto:[email protected]>

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Font woes in Debian with latest nightly builds
by Miguel Ortiz Lombardía 20 Jan '15

20 Jan '15

Hi, I recently updated from dev-1805 to dev-1924 (in both cases I used CentOS5 installers for a Debian testing -jessie- machine; dev-1922 gave the same problem) During installation I observed these messages: <...> updating fonts/local.conf file running mkfontdir Couldn't determine weight for Vera.pfa Couldn't determine weight for VeraMono.pfa rebuilding font cache Fontconfig error: Cannot load default config file /usr/local/phenix-dev-1922/base/bin/fc-cache: "/usr/local/phenix-dev-1922/base/share/fonts": skipping, no such directory /usr/local/phenix-dev-1922/base/bin/fc-cache: succeeded <...> I found a previous post to this list with a similar report (january 29, 2013) but there it was said that these messages could be ignored... However, when I run phenix I see these in the terminal: $ phenix Linux /usr/local/phenix-dev-1922/build/bin/phenix: 109: [: Linux: unexpected operator Fontconfig error: Cannot load default config file Phenix data directory: /home/ortiz-lombardia/Phenix (python2.7:11563): Pango-WARNING **: No builtin or dynamically loaded modules were found. Pango will not work correctly. This probably means there was an error in the creation of: '/home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos5/base/etc/pango/pango.modules' You should create this file by running pango-querymodules. (python2.7:11563): Pango-WARNING **: pango_shape called with bad font, expect ugly output (python2.7:11563): Pango-WARNING **: pango_font_get_glyph_extents called with null font argument, expect ugly output (python2.7:11563): Pango-WARNING **: pango_font_get_metrics called with null font argument, expect ugly output (python2.7:11563): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos5/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (python2.7:11563): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos5/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (python2.7:11563): Gtk-WARNING **: Error loading theme icon for stock: Couldn't recognize the image file format for file '/usr/share/icons/gnome/48x48/status/gtk-dialog-error.png' (python2.7:11563): Pango-WARNING **: _pango_cairo_font_install called with bad font, expect ugly output ^C Indeed, it is ugly output... No readable text just little empty boxes. I can send a snapshot if required. If I run: dpkg -l \*pango\* un gir1.0-pango-1 <none> <none> (no description available) ii gir1.2-coglpan 1.18.2-3 amd64 GObject introspection data for th ii gir1.2-pango-1 1.36.8-3 amd64 Layout and rendering of internati ii libcogl-pango2 1.18.2-3 amd64 Object oriented GL/GLES Abstracti ii libpango-1.0-0 1.36.8-3 amd64 Layout and rendering of internati ii libpango-perl 1.226-2 amd64 Perl module to layout and render ii libpango1.0-0: 1.36.8-3 amd64 Layout and rendering of internati ii libpango1.0-de 1.36.8-3 amd64 Development files for the Pango un libpango1.0-do <none> <none> (no description available) ii libpangocairo- 1.36.8-3 amd64 Layout and rendering of internati ii libpangoft2-1. 1.36.8-3 amd64 Layout and rendering of internati ii libpangomm-1.4 2.34.0-1.1 amd64 C++ Wrapper for pango (shared lib ii libpangox-1.0- 0.0.2-5 amd64 pango library X backend ii libpangox-1.0- 0.0.2-5 amd64 pango library X backend - develop ii libpangoxft-1. 1.36.8-3 amd64 Layout and rendering of internati un pango-graphite <none> <none> (no description available) un pango1.0-multi <none> <none> (no description available) Also, dpkg -l \*fontconfig\* produces: ii fontconfig 2.11.0-6.3 amd64 generic font configuration librar ii fontconfig-con 2.11.0-6.3 all generic font configuration librar un libfontconfig <none> <none> (no description available) un libfontconfig- <none> <none> (no description available) ii libfontconfig1 2.11.0-6.3 amd64 generic font configuration librar ii libfontconfig1 2.11.0-6.3 i386 generic font configuration librar ii libfontconfig1 2.11.0-6.3 amd64 generic font configuration librar I would appreciate any clues to solve this issue. Cheers, Miguel

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Bug in phenix.carbo_load in latest nightlies
by Roger Dodd 20 Jan '15

20 Jan '15

Hi all, I've been using the carbo_load tool to add in GlcNAc residues to Asn side chains and have noticed that in recent nightlies there is a bug that throws up the following error message (this occurs even if carbo_load is just run in "mode 1"): Traceback (most recent call last): File "/Applications/phenix-dev-1924/build/../modules/elbow/elbow/command_line/carbo_load.py", line 705, in <module> run(args) File "/Applications/phenix-dev-1924/build/../modules/elbow/elbow/command_line/carbo_load.py", line 417, in run from elbow.saccharide import carbohydrate_classes File "/Applications/phenix-dev-1924/modules/elbow/elbow/saccharide/carbohydrate_classes.py", line 28, in <module> from phenix.ligands.DensityBlobsClassConnectivity import DensityBlobsClassConnectivity ImportError: No module named DensityBlobsClassConnectivity I get this with dev-1894 and dev-1924 but not the last stable 1.9-1692. Cheers, Roger -- Roger B. Dodd, PhD Cambridge Institute for Medical Research University of Cambridge School of Clinical Medicine Wellcome Trust/MRC Building Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY

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Molecular replacement with fixed solution
by Muhammed bashir Khan 19 Jan '15

19 Jan '15

Hi There; I want to solve the structure with molecular replacement using phaser in phenix GUI. When I get solution from the one, how I can use as it as already solution using phenix in the next run. I use the "ensamble is fixed partial solution" but seems its not working. Any suggestion will be highly appreciated. Thanks Regards -- Muhammad Bashir Khan ************************************************** Department for Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Austria Phone: +43(1)427752224 Fax: +43(1)42779522

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sudden increase of clashscore
by Smith Lee 19 Jan '15

19 Jan '15

Dear All, In a Phenix refinement, with refinement settings as default in the graphics interface, at 2' rsrl stage the clashscore suddenly increases to more than 50, and then gradually decreases to lower than 20. Will you please tell me why this can occur? And what its effect on the refinement? Smith

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Re: [phenixbb] questions related to Phenix refinement
by Kay Diederichs 18 Jan '15

18 Jan '15

Dear Pavel, Am 18.01.15 um 07:23 schrieb phenixbb-request(a)phenix-online.org: > Date: Sat, 17 Jan 2015 20:36:30 -0800 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: Smith Lee <smith_lee123(a)yahoo.com>, "phenixbb(a)phenix-online.org" > <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] questions related to Phenix refinement > Message-ID: <54BB384E.30602(a)lbl.gov> > Content-Type: text/plain; charset="windows-1252"; Format="flowed" > > Hello Smith, > >> > In the X-ray statistics by resolution bin of the Phenix.refine result, >> > there is a column "%complete". For my refinement data, I find the >> > better the resolution (from lower resolution to the higher >> > resolution), the lower the completeness (for example for 40-6 A, >> > %complete is 98, for 3.1-3.0 A, %complete is 60%, for 2.2-2.1 A, >> > %complete is 6%). >> > >> > Will you please tell me what does this "%complete" mean? why it >> > decreases in the better diffraction bin? > Completeness is how many reflections you have compared to theoretically > possible. So the higher completeness the better. Ideally (and it's not > that uncommon these days) you should have 100% complete data set in > d_min-inf resolution. Anything below say 80 in any resolution bin is > bad, and numbers you quote 6-60% mean something is wrong withe the dataset. > Given your standing in the community, the last sentence will lead many unexperienced people to believe that they should cut their data at the resolution where the completeness falls below "say 80"%. But that would be wrong. There is no reason to consider a completeness as "too low in a high-resolution shell" as long as the data in that shell are good. Particularly in refinement any reflection helps to improve the model, and to reduce overfitting. Of course, more complete is better! Nowadays there should be no reason _not_ to get >95% (>99% in high-symmetry spacegroups) completeness in the low resolution shells, unless people stick to the "collect minimum rotation range" paradigm, and get the starting angle (or the point group!) wrong. best, Kay

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FW: question regarding Table1
by SD Y 18 Jan '15

18 Jan '15

From: ccp4_sc(a)hotmail.com To: phenixbb-request(a)phenix-online.org Subject: question regarding Table1 Date: Fri, 16 Jan 2015 20:30:47 -0600 Hi Everyone, I used phenix refined pdb, mtz and original mtz in the latest version of phenix to generate Table 1 and I felt the following was not right. I am not sure of the reason. R-merge 1.193e-17 (1.036e-17) R-meas 1.688e-17 CC1/2 1 (1) CC* 1 (1) Let me know . I appreciate your comments. Regards,SDY

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questions related to Phenix refinement
by Smith Lee 18 Jan '15

18 Jan '15

Dear All, In the X-ray statistics by resolution bin of the Phenix.refine result, there is a column "%complete". For my refinement data, I find the better the resolution (from lower resolution to the higher resolution), the lower the completeness (for example for 40-6 A, %complete is 98, for 3.1-3.0 A, %complete is 60%, for 2.2-2.1 A, %complete is 6%). Will you please tell me what does this "%complete" mean? why it decreases in the better diffraction bin? For the Ramachandran restrain in the Phenix.refine, there was a recommendation that for good resolution (I forget how much exactly, maybe 2.5 A), do not use Ramachandran restrain. But for a crystal data with resolution better than 1.5 A, in the X-ray statistics by resolution bin of the Phenix.refine result, there are more rows with resolution poorer than the defined 2.5 A (for example 40-6 A,6-3 A), although the crystal has a resolution better than 1.5 A (for example 1.4 A), can I use Ramachandran restrain in the Phenix.refine in this situation? If I use Ramachandran restrain in the Phenix.refine, I find the R-work and R-free level goes up, can we say the strategy of Ramachandran restrain in my refinement was not appropriate? I am looking forward to getting your reply. Smith

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Xray / neutron joint refinement
by Anna Makal 16 Jan '15

16 Jan '15

Hi, I have just done a joint x-ray / neutron refinement in Phenix using 5PTI structure and data from PDB. The input contains H atoms, with positions as refined against neutron dataset. In the resulting model, all H atoms ended up in 'idealized X-ray' positions (C-H distance of 0.96A), just as they would if I performed refinement against xray data only with riding model for H hydrogen atoms. Is it possible to run joint X-ray neutron refinement in such a manner that final H atoms positions are based on neutron data? Regards, Anna Makal

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Phenix - Research Scientist Position
by Paul Adams 15 Jan '15

15 Jan '15

Lawrence Berkeley Laboratory Career-track Research Scientist Job ID: 80447 Division: Physical Biosciences Date Opened: 1/14/2015 https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=80447 Summary: A research scientist position is available to work on developing new methods for macromolecular structure determination and refinement with the PHENIX software system. To learn more about Phenix visit: http://www.phenix-online.org Duties: This position will develop and maintain a powerful graphical user interface for the PHENIX system, and develop code within the Computational Crystallography Toolbox (cctbx). This position will include the development of new methods for crystallographic structure determination and completion in the context of the PHENIX program. This position also has a significant responsibility for the maintenance of PHENIX automated compilation tools, web-based interfaces for software downloads and coordinating releases of Phenix to the user community. The incumbent will work under the general direction of the Principal Investigator (PI; Paul Adams) for this project. Duties will also include testing, documentation writing, and extensive interaction with users and other developers. Qualifications: Demonstrated expertise with computational methods for protein crystallography. First-author publications in the area of macromolecular crystallography. Familiarity with software development: C++ and the Python scripting language. Advanced knowledge of Python-based or similar graphical user interface development tools. Solid interpersonal skills and the ability to work in a team environment are critical. A Ph.D. in computational crystallography, biophysics, chemistry, computer science, or related field is strongly preferred. Note that this is a multi-year position that is renewed annually on the basis on performance and continued funding. Berkeley Lab addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age or protected veteran status. Learn more at http://www.lbl.gov. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 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: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Reducing R/R-free
by George D 14 Jan '15

14 Jan '15

Hi Phenix users, I was looking at the phenix-refine manual and it mentions running optimize_mask=true optimize_xyz_weight=true optimize_adp_weight=true I was wondering what else I could try to bring the Rw/Rf down by 1-2% if possible, just wondering if there are any other strategies I could try. Thank you, George

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phenix.pdb_as_cif
by jp d 14 Jan '15

14 Jan '15

hi,of course, i should have included the versionphenix.version_1.9-1692 the pdb has done more digging and included this comment "Aside from the asym_id, there is another way we use for the mapping, _atom_site_anisotrop.id should map(for ANSIO) to _atom_site.id(for ATOM). This is one-by-one match for each atom. If you look at the file, you see that in the ATOM section, you have ATOM 99999 N3 . U . 367 ? -23.56200 29.36600 106.68800 1.000 135.52000 N ? UC ? 11964 1 ATOM 100000 C4 . U . 367 ? -23.35700 30.62600 106.16100 1.000 133.22000 C ? UC ? 11964 1 But in the ANISO section, you have 99999 N3 . U . 367 ? 2.04230 1.43260 1.67410 -0.19220 -0.28280 -0.16500 A0000 C4 . U . 367 ? 2.00150 1.41600 1.64420 -0.1 8730 -0.28010 -0.16450 i.e. the atom No. after 99999 is inconsistent between the two sections. The ANISO should use 100000. " thanksjpd

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Importing project to Phenix
by Emilia C. Arturo (Emily) 14 Jan '15

14 Jan '15

Hello, I'd like to take a phenix project (on which I've been working successfully on the Mac where I initially created the project) from one Mac to another Mac. When I tried to use the 'Import project' tool on the new computer, I got a notification that "[...] the directory must contain the PHENIX project tracking data (a sub-directory named 'phenix' or '.phenix', and associated files)." Unfortunately, I didn't see a sub-directory named 'phenix' or '.phenix' in the folder where all my project files had been created and stored, and wasn't sure what to do about it, so I proceeded with the Import anyway, to see what would happen. On the new computer, the project was imported seemingly successfully (e.g. the project history is all there), but when I tried to Run a refinement I'd configured for this project, I got an error about the missing '.phenix' file. The error is: "Cannot open file for write: [...] No such file or directory: [...]/.phenix/project_data/refine_22.eff' Can someone help me figure out how to properly move a project from one computer to another? Thank you, Emily.

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pdb_as_cif
by jp d 14 Jan '15

14 Jan '15

hi,I am making a large deposit to the pdb. To convert it to cif i usedphenix.pdb_as_cif model.pdb it looks like the ANISOU lines lose chain information.the PDB responded with this comment "The model coordinates file you output from Phenix is not complete. In the cif format file you deposited, if you look at the cif item _atom_site_anisotrop.pdbx_auth_asym_id, i.e. the column 5 of the Aniso section, you see value for every atom is dot ("."). The _atom_site_anisotrop.pdbx_auth_asym_id is just like the chain ID in the legacy PDB format, it should be consistent with the values of cif item _atom_site.auth_asym_id in the xyz section, otherwise there is no way to map between xyz Cartesian values and aniso values that are now separated in two sections." Do you reccomend another way to convert it to cif ? Thanksjpd

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map coefficients file
by Dialing Pretty 14 Jan '15

14 Jan '15

Dear All, Will you please tell me the subfixer of the map coefficients file, or which file is the map coefficients file? Dialing

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Applications for RapiData 2015 are now open
by Thomas Eriksson 13 Jan '15

13 Jan '15

The 2015 RapiData Course on Data Collection and Structure Solution will take place at the Stanford Synchrotron Radiation Lightsource (SSRL) from May 3-8 2015. The aim of the course is to educate and train scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on sample preparation, data collection and reduction, phasing and complementary methods. For a more complete description of the course goals and format see http://www-ssrl.slac.stanford.edu/conferences/rapidata-2015/about.html The deadline for applications is February 23rd 2015. To apply follow this link: http://www-ssrl.slac.stanford.edu/conferences/rapidata-2015/apply.php Several scholarships are available from the International Union of Crystallography to cover partial travel and subsistence for Latin-American students, postdocs and junior faculty. Additional funds may be also be awarded to other participants (no restrictions) on a per need basis. Interested participants should apply for the course, and contact the organizers, enclosing a letter of recommendation from their supervisor. The Organizing Committee of RapiData2015 shall observe the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist which would prevent the participation of bona fide scientists. Ana Gonzalez and Clyde Smith -- ------------------------------------------- Ana Gonzalez <ana(a)slac.stanford.edu> Staff Scientist Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Road, MS 99 Menlo Park CA 94025 Phone: (650) 926 8682 Fax: (650) 926 3292 -------------------------------------------

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Rosetta MR mmcif file subprocess failed
by Christian Roth 12 Jan '15

12 Jan '15

Hi phenix developers, I started a Rosetta MR run with a model pdb and the target sequence file. It seems that the initial MR run went fine and the Rebuilding Job for the best MR solution started. A sequence alignment is shown in the log file and than the job stops suddenly with the message Sorry: mmcif file must contain at least one data block. I can't even find a mmcif file in one of the folders. Any idea what might went wrong. Thanks in advance for your help. Christian

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6th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 12 Jan '15

12 Jan '15

Firth announcement 6th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 1 - June 5, 2015 Application deadline: April 10, 2015 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization is not able to support travel or accommodation. The number of participants will be limited to 15. There is no registration fee for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 10, 2015. Detailed information can be found on the workshop web page: https://public.ornl.gov/neutrons/conf/gcnb2015. Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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Rw/Rf -phenix - wwPDB Validation Server
by Haytham Wahba 11 Jan '15

11 Jan '15

1- after getting structure refined with phenix.refine to 0.145 , 0.164 Rw/Rf. and then you feel happy with that. then after using validation server from PDB you get 0.158 , 0.181 Rw/Rf. why this big jump for R free. why phenix.refine giving us low R free where in reality is not? 2- if i want to show kick map for metal binding site for publication, which map and how could i generate it. thank you for your help. HWUdeM

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A question related to phenix refine
by Dialing Pretty 11 Jan '15

11 Jan '15

Dear All, In a Phenix refinement process, the RMS angles fluctuates between 1.50 and 1.60, i..e., it does not decrease gradually. Can I accept the refinement result or not, and why? I am looking forward to getting a reply from you. Dialing.

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