- 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

2 1

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

2 2

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 >

5 4

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/>

1 0

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

2 1

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

3 8

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

1 0

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

3 2

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

2 3

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.

1 0