- phenixbb - phenix-online.org

No Sigmas in Phenix Refinement?
by Keller, Jacob 29 Jan '16

29 Jan '16

Dear Phenix Team, I heard a rumor that Phenix does not use experimental sigmas in refinement--is this true? JPK

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Re: [phenixbb] ligand modification / combination in REEL
by andre.stiel 28 Jan '16

28 Jan '16

Nigel, crazy thing, I repeated the ELBOW run with the exact same smiles for: 1.10-2155 and 1.10.1-2155 and it gives different results. With the newer version addressing the sugar correctly, as you said. Thanks! André André C. Stiel, Ph.D. (PI) +49 (0) 89 3187 3972 Office: Building 57, Room 009 Cell Engineering Group Institute of Biological and Medical Imaging > Am 21.01.2016 um 19:12 schrieb Nigel Moriarty <nwmoriarty(a)lbl.gov>: > > Andre > > I note that you use 1.10-2155. It works correctly with the latest nightly build. You could also try 1.10.1-2155 if you are more comfortable with major releases. Version 1.10-2155 was replaced with 1.10.1-2155. > > Cheers > > Nigel > > --- > Nigel W. Moriarty > Building 33R0349, Physical Biosciences Division > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov <http://cci.lbl.gov/> > On Wed, Jan 20, 2016 at 11:51 PM, andre.stiel <andre.stiel(a)helmholtz-muenchen.de <mailto:[email protected]>> wrote: > Hi Nigel, > thanks for your time, here you go. And I attached the .cif I obtain from ELBOW > > Helmholtz Zentrum Muenchen > Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) > Ingolstaedter Landstr. 1 > 85764 Neuherberg > www.helmholtz-muenchen.de <http://www.helmholtz-muenchen.de/> > Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe > Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) > Registergericht: Amtsgericht Muenchen HRB 6466 > USt-IdNr: DE 129521671 > > > > http://www.chemspider.com/Chemical-Structure.28639235.html?rid=ac73301e-ee9… <http://www.chemspider.com/Chemical-Structure.28639235.html?rid=ac73301e-ee9…> > CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O[C@@H]1[C@@H]([C@@H]([C@H]([C@@H]([C@H]1O)O)O)O)O)OC(=O)CCCCCCC/C=C\C/C=C\CCCCC > > cheers > André > > >> Am 20.01.2016 um 21:40 schrieb Nigel Moriarty <nwmoriarty(a)lbl.gov <mailto:[email protected]>>: >> >> Its is very strange that the SMILES string is resulting in an aromatic ring. Can you send me the SMILES? >> >> Cheers >> >> Nigel >> >> --- >> Nigel W. Moriarty >> Building 33R0349, Physical Biosciences Division >> Lawrence Berkeley National Laboratory >> Berkeley, CA 94720-8235 >> Phone : 510-486-5709 <tel:510-486-5709> Email : NWMoriarty(a)LBL.gov <mailto:[email protected]> >> Fax : 510-486-5909 <tel:510-486-5909> Web : CCI.LBL.gov <http://cci.lbl.gov/> >> On Sat, Jan 9, 2016 at 3:38 AM, andre.stiel <andre.stiel(a)helmholtz-muenchen.de <mailto:[email protected]>> wrote: >> Hi, >> >> I have a phosphatidyl inositol ligand without an existing CIF file only smiles. When I construct the ligand from the smiles ELBOW regards the sugar as just an aromatic ring. >> So I see three possibilities how to end up with a proper constraints file for my ligand (that is: tails like in the smiles but with a proper sugar (chair) conformation on top): >> 1. Can I edit the aromatic ring in REEL in a way to push it into the desired boat/chair conformation? I did not find a command to that end although he can clearly „see“ this conformation as I know from another ligand. >> 2. Can I chop the sugar part from the .CIF of another ligand and somehow fuse it to my tails? >> 3. There is a sugar editor in REEL (which however crashes at the moment for me (Version 1-10-2155)) can I use this to construct the desired sugar and somehow fuse it to the rest… basically like option 2? >> I have not found a very extensive documentation on how to play such tricks with REEL. >> Or would I have to rebuild a complete ligand with this SCALES? >> >> Other suggestion how to get my ligand are also welcome. >> >> Thanks >> >> André >> >> Helmholtz Zentrum Muenchen >> Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) >> Ingolstaedter Landstr. 1 >> 85764 Neuherberg >> www.helmholtz-muenchen.de <http://www.helmholtz-muenchen.de/> >> Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe >> Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) >> Registergericht: Amtsgericht Muenchen HRB 6466 >> USt-IdNr: DE 129521671 >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb <http://phenix-online.org/mailman/listinfo/phenixbb> >> Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]> > > > Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671

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7th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 27 Jan '16

27 Jan '16

First announcement 7th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. May 16 - May 20, 2016 Detailed information can be found on the workshop web page: https://conference.sns.gov/event/15 Application deadline: April 1, 2016 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 1, 2016. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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Faculty Positions in Structural Biology at Purdue University
by Noinaj, Nicholas 26 Jan '16

26 Jan '16

PHENIXbb, I wanted to bring to your attention that our Structural Biology group here at Purdue University is looking to hire three new faculty members at the Assistant (tenure-track), Associate, and Full Professor ranks, as outlined in the job ad. The official ad from Science can be accessed via this link (copied below as well): http://jobs.sciencecareers.org/job/391248/faculty-positions-in-structural-b… It is important to also add that Purdue University has just made a HUGE investment of more than $250 million to life sciences over the next five years to advance research. http://www.purdue.edu/newsroom/releases/2016/Q1/purdue-to-invest-more-than-… As a new faculty member myself, I can attest that Purdue is an amazing place to do research! We have all the resources needed to do cutting-edge studies in structural biology on many types of projects including drug discovery, enzymes, viruses, protein assemblies and complexes, membrane proteins, and more. Please forward this email to others who may be interested and/or actively looking for a faculty position, but not on PHENIXbb or CCP4bb. Thanks in advance! Cheers, Nick ------------------------------- Nicholas Noinaj 240 S. Martin Jischke Dr. Hockmeyer Building of Structural Biology, Rm 333 Dept. of Biological Sciences, Purdue Univ. West Lafayette, IN 47907 765-496-0061 (office) 765-496-0059 (wetlab) +++++++++++++++++ Faculty Positions in Structural Biology Markey Center for Structural Biology Department of Biological Sciences The Department of Biological Sciences, Purdue University, is initiating a major effort to expand its investment in Structural Biology and invites applicants at all academic professorial levels to fill multiple new tenure-track faculty positions in this accelerating area. The Structural Biology Group at Purdue is recognized worldwide for its leadership in structural biology of viruses, membrane proteins, and technical approaches to crystallographic and electron microscopy challenges. Creative investigators in a variety of research approaches, X-ray crystallography, NMR spectroscopy and electron microscopy, are sought to enhance these current structural investigations. Potential areas of research interest include but are not limited to studies of viruses and other pathogens, membrane proteins, cancer biology, target molecules for structure-based drug discovery and development of new technologies in structural biology. This position is aligned with major campus-wide investments in the life sciences including the Center for Drug Discovery (https://www.purdue.edu/research/pcdd/), the Center for Integrative Neurosciences and the Institute for Inflammation, Immunology and Infectious Disease (https://www.purdue.edu/research/life-sciences/). Applicants for senior positions in Structural Biology must have a Ph.D. or equivalent in an appropriate discipline and currently hold a position equivalent to an Associate or Full Professor. Structural biologists with a clear cancer focus in their research will also be considered by the Purdue Center for Cancer Research as a Walther Cancer Professor (https://www.cancerresearch.purdue.edu). Applicants at the junior rank in Structural Biology must have a Ph.D. or equivalent in an appropriate discipline and at least 2 years of postdoctoral experience. There is particular interest in researchers trained in single particle cryo-electron microscopy or whole cell electron tomography. Successful applicants for these positions are expected to direct a dynamic and collaborative research program in structural biology to address fundamental questions in the area of human disease, to excel at teaching at the undergraduate and/or graduate level and participate in ongoing programs at Purdue. Extensive opportunities for collaboration exist within the Department, which has over 50 faculty members conducting research in neurobiology, virology, microbiology, molecular and cell biology, bioinformatics, evolutionary biology and ecology (http://www.bio.purdue.edu/). These opportunities are enhanced by a highly interactive community of scientists within the Colleges of Science, Pharmacy, Veterinary Medicine and Engineering and existing and emerging interdisciplinary centers in the life sciences. Abundant infrastructure support for structural biology exists, including advanced imaging analysis and biophysical instrumentation available in established core facilities at the Bindley Bioscience Center and the Birck Nanotechnology Center in Discovery Park (http://www.purdue.edu/discoverypark/). Applications should be submitted electronically to https://hiring.science.purdue.edu/ as a single PDF file containing a letter of interest, a detailed curriculum vitae, contact information for three references, a two to three page summary of research interests, and a one-page teaching statement. The Department of Biological Sciences is committed to advancing diversity in all areas of faculty effort - scholarship, instruction and engagement. Candidates should address at least one of these areas in their cover letter, including past experience, current activity and/or future goals to promote a climate that values diversity and inclusion. As an ADVANCE institution, Purdue University is dedicated to the recruitment, retention and advancement of women in the STEM disciplines. Inquiries should be directed to Cynthia Stauffacher, Chair, Structural Biology Search Committee StructureSearch(a)bio.purdue.edu<mailto:[email protected]> Structural Biology Search Committee Department of Biological Sciences Purdue University, 915 W. State St., West Lafayette, IN 47907-2054. Review of applications will begin December 15, 2015 and continue until these positions are filled. A background check is required for employment in this position. Purdue University is an EOE/Affirmative Action Employer. All qualified applicants, including minorities, women, individuals with disabilities and veterans are encouraged to apply. +++++++

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postdoctoral position MRC Laboratory of Molecular Biology
by Roger Williams 26 Jan '16

26 Jan '16

A three-year postdoctoral position is available with the group of Roger Williams at the MRC Laboratory of Molecular Biology in Cambridge, UK. The project, which is funded by Cancer Research UK is aimed at understanding structural mechanisms of regulation of the target of rapamycin complexes. Specifically to undertake research to investigate the structures and regulation of the mTORC1 complex assembled with its regulators on lysosomal membranes. The objective is to determine the structures of mTORC1 in complexes with its regulators and to understand how these complexes assemble on lysosomal membranes. Methods involved in the study include large scale mammalian cell culture, cryo-electron microscopy; X-ray crystallography; hydrogen-deuterium exchange mass spectrometry; biophysical measurements of assembly on membranes by confocal microscopy, flow cytometry and single-molecule fluorescence; and enzyme assays. The candidate should have a Ph.D. degree or due to complete doctoral studies within 6 months of applying. It is essential that the candidate has an enthusiasm for structural biology. Experience with electron microscopy, X-ray crystallography, mass spectrometry or large scale eukaryotic expression systems would be desirable, but a motivated candidate could learn any or all of these. The MRC Laboratory of Molecular Biology is one of the birthplaces of modern molecular biology and has amazing support for all aspects of structural biology. For full details, see the MRC link https://mrc.tal.net/vx/mobile-0/appcentre-ext/brand-3/candidate/so/pm/4/pl/… <https://mrc.tal.net/vx/mobile-0/appcentre-ext/brand-3/candidate/so/pm/4/pl/…> or contact Roger Williams: email rlw(a)mrc-lmb.cam.ac.uk <mailto:[email protected]> or phone: +44 1223 267094 Dr. Roger Williams, FMedSci rlw(a)mrc-lmb.cam.ac.uk <mailto:[email protected]> MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH UK Phone: +44 1223 267094

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Job opportunity at the NKI
by Anastassis Perrakis 26 Jan '16

26 Jan '16

We are looking for an enthusiastic co-worker who recently got a PhD in Structural Biology and has strong working experience in X-ray crystallography and a clear interest in cell biology mechanisms, aspiring to connect molecular chemistry and structure to the inner workings of a cell, using a wide portfolio of approaches. You will study with us the mechanisms that ensure correct chromosome segregation during cell division in a project with a two-fold scope. First, in collaboration with the group of Geert Kops (Hubrecht Institute) we want to determine new structures and understand the function of proteins that control spindle checkpoint signaling. Second, in collaboration with the EMBL Grenoble Unit and the Diamond Light Source in the iNEXT (www.inext-eu.org <http://www.inext-eu.org/>) project, we want to establish, benchmark and extend fragment-based screening, using as our major targets mitotic proteins we work on. The two projects are scientifically coherent and significant preliminary work is in place. You will be responsible for designing and executing all experiments as part of a small but lively team. The project will be supported by the NKI Protein Facility and state of the art instrumentation for expressing, purifying and crystallising proteins (including robotics), as well as a wealth of biophysical equipment, including surface plasmon resonance, microscale thermophoresis, isothermal titration calorimetry, fluorescence measurement, and light scattering. The NKI also offers a Robotics and Screening Centre, a Genomics core, Proteomics, Peptide synthesis, and Microscopy facilities. The group is hosted in the Department of Biochemistry, a diverse and lively environment with enthusiastic colleagues. The NKI is an integrated hospital and research centre for cancer, and is located within minutes from the centre of Amsterdam and it’s cultural amenities. The temporary employment will be for an initial period of 2 years. The gross salary per month will be ~3,300 Euro, according to the FWG-function group 55.6, or higher depending on previous experience. Foreigners are entitles to a 30% tax break, subject to a decision of the tax authorities. For further information please contact Anastassis Perrakis, a.perrakis(a)nki.nl <mailto:[email protected]>, or send directly your CV including the names of three referees, no later than 19 February. Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

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Re: [phenixbb] [ccp4bb] Modify methionine to acetylated methionine in coot
by Anshul Bhardwaj 26 Jan '16

26 Jan '16

Thanks Paul for the quick response. Simple enough and works beautifully for modifying N-terminus methionine to AME in coot. Anshul Bhardwaj ________________________________________ From: Paul Emsley <pemsley(a)mrc-lmb.cam.ac.uk> Sent: Monday, January 25, 2016 7:39 PM To: Anshul Bhardwaj; COOT(a)jiscmail.ac.uk Subject: Re: [ccp4bb] Modify methionine to acetylated methionine in coot On 25/01/2016 23:33, Anshul Bhardwaj wrote: > Hello, Hello. > How to replace 'M' with 'AME' in coot itself? an option like mutate residue, etc. > I couldn't figure out right away so I worked my way around by simply copying AME from one of the pdb from RCSB database and replaced methionine in my model. Linked AME to residue# 2 in coot and refinement was straightforward after generating restraints for the modified model. So it worked for now but still curious as there has to be a way to replace 'M' with 'AME' in coot, isn't it (?). > Generally, for this sort of thing one would use: Extensions -> Modelling -> Replace Residue -> AME But this might not work in the case because the modification is on the main-chain not the side-chain. But it might do if the AME is at the N-terminus. This thread might shed some light on things: https://www.mail-archive.com/[email protected]/msg02536.html Paul. The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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Modify methionine to acetylated methionine in coot
by Anshul Bhardwaj 25 Jan '16

25 Jan '16

Hello, How to replace 'M' with 'AME' in coot itself? an option like mutate residue, etc. I couldn't figure out right away so I worked my way around by simply copying AME from one of the pdb from RCSB database and replaced methionine in my model. Linked AME to residue# 2 in coot and refinement was straightforward after generating restraints for the modified model. So it worked for now but still curious as there has to be a way to replace 'M' with 'AME' in coot, isn't it (?). Thanks, Anshul Bhardwaj P.S. Hope it's okay to cross-post on both ccp4bb and phenixbb to get an answer quickly. The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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Coot 3D for Geforce GTX 970 Graphics card on Windows 7 and Fedora
by Xiao Lei 25 Jan '16

25 Jan '16

Hi Phenixbb members, My lab has a desktop PC which has Windows 7 with Geforce GTX 970 Graphics card, is this card ok for the Coot 3D function with 3D monitor and Nvidia 3D kit? Do I need to do some settings before I can use the Coot 3D function? I'm also thinking installing Fedora 23 on the PC and use coot 3D, is there any settings in the Fedora environment before using coot 3D? Thanks ahead.

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Changing NCS groups
by Marie Elizabeth Fraser 25 Jan '16

25 Jan '16

Hello, I would like to edit the NCS information for a model with two chains. I've tried running find_ncs and editing the phil file, but I get an error when I try to use my edited file in the next cycle of refinement. I've tried using the utility to detect NCS groups, then edited in the little windows - also no success. How are other people defining NCS when they aren't content with the equivalences the program finds? Thank you for your insight, Marie

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Xtriage systematic results is not consistent with HKL2000
by Alex Lee 23 Jan '16

23 Jan '16

Dear All, I scaled a dataset of SG P2221 in HKL2000 and got systematic absence results as below, it seems clearly HKL2000 showed the data had systematic absence violations, but when I used the .sca file from HKL2000 as input in Xtriage, the result did not show any systematic violations. Which result should I rely on? HKL200 Results: Summary of reflections intensities and R-factors by shells R linear = SUM ( ABS(I - <I>)) / SUM (I) R square = SUM ( (I - <I>) ** 2) / SUM (I ** 2) Chi**2 = SUM ( (I - <I>) ** 2) / (Error ** 2 * N / (N-1) ) ) In all sums single measurements are excluded Shell Lower Upper Average Average Norm. Linear Square limit Angstrom I error stat. Chi**2 R-fac R-fac Rmeas Rpim CC1/2 CC* 50.00 5.60 2819.0 103.7 44.8 0.607 0.033 0.040 0.037 0.017 0.998 0.999 5.60 4.45 1801.5 63.8 28.1 0.914 0.043 0.050 0.048 0.022 0.997 0.999 4.45 3.88 1435.3 52.6 25.5 0.980 0.048 0.051 0.054 0.024 0.997 0.999 3.88 3.53 738.7 31.8 20.5 1.117 0.068 0.067 0.075 0.032 0.996 0.999 3.53 3.28 489.7 26.5 20.1 1.134 0.092 0.080 0.102 0.043 0.996 0.999 3.28 3.08 236.3 19.8 17.4 0.975 0.147 0.108 0.162 0.069 0.993 0.998 3.08 2.93 93.4 16.4 16.0 0.850 0.296 0.277 0.327 0.138 0.947 0.986 2.93 2.80 62.9 16.3 16.0 0.737 0.422 0.384 0.467 0.197 0.921 0.979 2.80 2.69 42.6 16.7 16.5 0.677 0.622 0.515 0.688 0.291 0.879 0.967 2.69 2.60 29.3 20.0 19.9 0.680 0.924 0.842 0.000 0.440 0.659 0.891 All reflections 798.1 37.4 22.6 0.873 0.064 0.050 0.068 0.031 Intensities of systematic absences h k l Intensity Sigma I/Sigma 0 0 3 -0.4 1.3 -0.3 0 0 5 10.4 3.0 3.5 0 0 7 11.4 3.9 2.9 0 0 9 8.7 4.3 2.0 0 0 11 18.6 6.4 2.9 0 0 13 182.9 17.1 10.7 0 0 15 3.0 7.8 0.4 0 0 17 11.9 9.2 1.3 0 0 19 30.0 14.3 2.1 0 0 21 7.4 11.1 0.7 0 0 23 54.2 15.6 3.5 0 0 25 43.1 16.1 2.7 0 0 27 12.5 18.9 0.7 0 0 29 -16.6 20.9 -0.8 0 0 31 31.0 25.4 1.2 0 0 33 3.4 29.2 0.1 0 0 35 -24.2 32.0 -0.8 0 0 37 50.9 42.5 1.2 0 0 39 -53.3 66.4 -0.8 0 0 41 65.8 50.6 1.3 0 0 43 -24.3 46.8 -0.5 0 0 45 -6.1 48.3 -0.1 0 0 47 -14.8 45.8 -0.3 0 0 49 1.1 53.5 0.0 0 0 51 -7.9 64.2 -0.1 Phenix Xtriage Results: ----------Space group identification---------- Analyses of the absences table indicates a number of likely space group candidates, which are listed below. For each space group, the number of systematic absence violations are listed under the '+++' column. The number of non-absence violations (weak reflections) are listed under '---'. The last column is a likelihood based score for the particular space group. Note that enantiomorphic spacegroups will have equal scores. Also, if absences were removed while processing the data, they will be regarded as missing information, rather then as enforcing that absence in the space group choices. ------------------------------------------------------------------------------------- | space group | # absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score | ------------------------------------------------------------------------------------- | P 2 2 2 | 0 | 0.00 | 0.00 | 0 | 4 | 0.000e+00 | | P 2 2 21 | 0 | 0.00 | 0.00 | 0 | 4 | 0.000e+00 | | P 2 21 2 | 5 | 3.07 | 16.77 | 5 | 4 | 1.038e+01 | | P 2 21 21 | 5 | 3.07 | 16.77 | 5 | 4 | 1.038e+01 | | P 21 2 2 | 5 | 1.89 | 15.21 | 5 | 4 | 1.250e+01 | | P 21 2 21 | 5 | 1.89 | 15.21 | 5 | 4 | 1.250e+01 | | P 21 21 2 | 10 | 2.48 | 15.99 | 10 | 4 | 2.288e+01 | | P 21 21 21 | 10 | 2.48 | 15.99 | 10 | 4 | 2.288e+01 | ------------------------------------------------------------------------------------- ----------List of individual systematic absences---------- Note: this analysis uses the original input data rather than the filtered data used for twinning detection; therefore, the results shown here may include more reflections than shown above. P 2 2 2: no systematic absences possible P 2 2 21 (input space group): no absences found P 21 2 2 ( 5, 0, 0): i/sigi = 21.0 ( 7, 0, 0): i/sigi = 4.8 ( 9, 0, 0): i/sigi = 14.3 ( 11, 0, 0): i/sigi = 15.2 ( 13, 0, 0): i/sigi = 18.3 ( 15, 0, 0): i/sigi = 12.7 ( 17, 0, 0): i/sigi = 4.1 P 2 21 2 ( 0, 3, 0): i/sigi = 21.3 ( 0, 5, 0): i/sigi = 21.4 ( 0, 7, 0): i/sigi = 20.7 ( 0, 9, 0): i/sigi = 21.4 ( 0, 11, 0): i/sigi = 20.7 ( 0, 13, 0): i/sigi = 14.5 ( 0, 17, 0): i/sigi = 10.4 ( 0, 21, 0): i/sigi = 14.4 ( 0, 23, 0): i/sigi = 0.8 ( 0, 25, 0): i/sigi = 2.3 ( 0, 27, 0): i/sigi = 2.0 P 21 21 2 ( 0, 3, 0): i/sigi = 21.3 ( 0, 5, 0): i/sigi = 21.4 ( 0, 7, 0): i/sigi = 20.7 ( 0, 9, 0): i/sigi = 21.4 ( 0, 11, 0): i/sigi = 20.7 ( 0, 13, 0): i/sigi = 14.5 ( 0, 17, 0): i/sigi = 10.4 ( 0, 21, 0): i/sigi = 14.4 ( 0, 23, 0): i/sigi = 0.8 ( 0, 25, 0): i/sigi = 2.3 ( 0, 27, 0): i/sigi = 2.0 ( 5, 0, 0): i/sigi = 21.0 ( 7, 0, 0): i/sigi = 4.8 ( 9, 0, 0): i/sigi = 14.3 ( 11, 0, 0): i/sigi = 15.2 ( 13, 0, 0): i/sigi = 18.3 ( 15, 0, 0): i/sigi = 12.7 ( 17, 0, 0): i/sigi = 4.1 P 2 21 21 ( 0, 3, 0): i/sigi = 21.3 ( 0, 5, 0): i/sigi = 21.4 ( 0, 7, 0): i/sigi = 20.7 ( 0, 9, 0): i/sigi = 21.4 ( 0, 11, 0): i/sigi = 20.7 ( 0, 13, 0): i/sigi = 14.5 ( 0, 17, 0): i/sigi = 10.4 ( 0, 21, 0): i/sigi = 14.4 ( 0, 23, 0): i/sigi = 0.8 ( 0, 25, 0): i/sigi = 2.3 ( 0, 27, 0): i/sigi = 2.0 P 21 2 21 ( 5, 0, 0): i/sigi = 21.0 ( 7, 0, 0): i/sigi = 4.8 ( 9, 0, 0): i/sigi = 14.3 ( 11, 0, 0): i/sigi = 15.2 ( 13, 0, 0): i/sigi = 18.3 ( 15, 0, 0): i/sigi = 12.7 ( 17, 0, 0): i/sigi = 4.1 P 21 21 21 ( 0, 3, 0): i/sigi = 21.3 ( 0, 5, 0): i/sigi = 21.4 ( 0, 7, 0): i/sigi = 20.7 ( 0, 9, 0): i/sigi = 21.4 ( 0, 11, 0): i/sigi = 20.7 ( 0, 13, 0): i/sigi = 14.5 ( 0, 17, 0): i/sigi = 10.4 ( 0, 21, 0): i/sigi = 14.4 ( 0, 23, 0): i/sigi = 0.8 ( 0, 25, 0): i/sigi = 2.3 ( 0, 27, 0): i/sigi = 2.0 ( 5, 0, 0): i/sigi = 21.0 ( 7, 0, 0): i/sigi = 4.8 ( 9, 0, 0): i/sigi = 14.3 ( 11, 0, 0): i/sigi = 15.2 ( 13, 0, 0): i/sigi = 18.3 ( 15, 0, 0): i/sigi = 12.7 ( 17, 0, 0): i/sigi = 4.1 Thanks ahead

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Change of PHIL definitions in phenix.find_alt_orig_sym_mate
by R.D. Oeffner 22 Jan '16

22 Jan '16

I have changed the PHIL definitions in this program from AltOrigSymMates.moving_pdb to AltOrigSymMates.moving.pdb and from AltOrigSymMates.fixed_pdb to AltOrigSymMates.fixed.pdb. I'm not sure if it is being used elsewhere but let me know if you encounter an error due to this. Regards, Rob

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anomalous completeness from Phenix Xtriage result
by Alex Lee 22 Jan '16

22 Jan '16

Dear All, After check my data with Phenix Xtriage, I got a warning of "the anomalous completeness is 42.34%". I do not know if I need to pay attention to this? I did not do experimental phasing and I did not add heavy metal to my crystal nor there is selenium on my protein. I even don't know why I still get the anomalous signal. But from the detailed summary below I guess in my case it's not a problem? ----------Summary---------- File name: P2_rejoutput.sca Data labels: I(+),SIGI(+),I(-),SIGI(-) Space group: P 1 2 1 Unit cell: 72.255, 46.617, 134.086, 90, 90.052, 90 Data type: xray.intensity Resolution: 49.1682 - 2.5855 Anomalous: True Number of reflections (non-anomalous): 27184 Completeness (non-anomalous): 95.42% Number of reflections (all): 38285 Completeness (all): 69.98% Anomalous completeness: 42.34% Completeness (non-anomalous) is the completeness of the data after merging Friedel pairs. Completeness (all) is the completeness of the data before merging Friedel pairs. Completeness (anomalous) is the completeness of the anomalous data. The anomalous completeness is calcluated by dividing the number of measured acentric, Bijvoet mates by the total possible number of acentric indices. Completeness (non-anomalous) should be used to determine if there is sufficient data for non-anomalous purposes (refinement, model-building). A value greater than 90% is generally desired, while a value less than 75% is considered poor. Values in between will provide less than optimal results. Completeness (anomalous) should be used to determine if there is sufficient data for anomalous purposes (phasing, finding anomalous atoms, refinement of anomalous occupancies or scattering factors). A value greater than 80% is generally desired, while a value less than 50% is considered poor. Values in between will provide less than optimal results. Thanks.

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Specify a chain in Phenix Autobuild
by Xiao Lei 21 Jan '16

21 Jan '16

Hi Phenixbb members, I am using Phenix autobuild for a protein-DNA complex. There are three chains for protein (F, H, I) and two chains for DNA (A and B). I know Autobuild can only build one chain at a time and I'm only going to build chain F. In the autobuild GUI, I can find an option of Chain type "Auto", "protein" , "DNA" and "RNA". Is there a place in the GUI which I can specify only building protein chain "F"? Thanks ahead.

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ligand modification / combination in REEL
by andre.stiel 20 Jan '16

20 Jan '16

Hi, I have a phosphatidyl inositol ligand without an existing CIF file only smiles. When I construct the ligand from the smiles ELBOW regards the sugar as just an aromatic ring. So I see three possibilities how to end up with a proper constraints file for my ligand (that is: tails like in the smiles but with a proper sugar (chair) conformation on top): 1. Can I edit the aromatic ring in REEL in a way to push it into the desired boat/chair conformation? I did not find a command to that end although he can clearly „see“ this conformation as I know from another ligand. 2. Can I chop the sugar part from the .CIF of another ligand and somehow fuse it to my tails? 3. There is a sugar editor in REEL (which however crashes at the moment for me (Version 1-10-2155)) can I use this to construct the desired sugar and somehow fuse it to the rest… basically like option 2? I have not found a very extensive documentation on how to play such tricks with REEL. Or would I have to rebuild a complete ligand with this SCALES? Other suggestion how to get my ligand are also welcome. Thanks André Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671

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N-acetylgalactosamine lacking amide planarity restraint
by Tristan Croll 20 Jan '16

20 Jan '16

Hi, I'm refining a structure that includes an O-linked N-acetylgalactosamine (NGA) residue, and from the way it's behaving the N-acetyl amide clearly has no restraints on its planarity. It's currently twisted almost 45 degrees from planar despite having no close contacts. Cheers, Tristan

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how not to refine residue X?
by Murpholino Peligro 19 Jan '16

19 Jan '16

Hi. How to tell phenix.refine to leave residue X during refinement? I already tried in the .eff >>> strategy = *individual_sites *individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous sites { individual = not (chain A and resid 97) <<< But resid 97 is being moved to another position. I am using phenix.refine_1.10.1-2155 Thanks

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phenix.sort_heteroatoms produced duplicated residue number
by luzuok 13 Jan '16

13 Jan '16

Dear phenixbb, When I use phenix.sort_hetero_atoms to resort my pdb, there are duplicated residue number of water and aa in the output pdb. Is this a bug? As there are many number gaps water, how can I fix it? Best wishes! Lu -- 卢作焜南开大学新生物站A202 Lu Zuokun, Ph.D. Candidate College of Life Science, Nankai University

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pdbtools model_statistics: average B-factors
by wtempel 12 Jan '16

12 Jan '16

Hello, are the mean B-factors in the "ADP statistics" table occupancy-weighted, or perhaps weighted in any other way? If so, please could you provide the formula. Thank you. Wolfram Tempel

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phenix.refine with reference model
by Falk, Sebastian 08 Jan '16

08 Jan '16

Hi! I am currently building a 3.3 A structure of a large protein. I do have a reference model at much better resolution that has 58% sequence identity and 77% similarity. The structures are quite similar, there are only a few regions with insertions. However, phenix.refine does ‘accept’ the reference model and thus creates no torsion restraints. I also tried to run ProSmart in CCP4 but there the cut-off for the reference model is 75% sequence identity. I could not find any threshold for phenix.refine though. I am happy for any suggestion or tip how to include the reference model even though the sequence identity is not as high. Thank a lot. Sebastian Sebastian Falk Max-Planck-Institute for Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany sfalk(a)biochem.mpg.de

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Generate sequence files of homodimer protein or double strand DNA for phaser MR
by Alex Lee 08 Jan '16

08 Jan '16

Dear Phenixbb members, I am using Phaser MR for solving a homodimer DNA binding protein with dsDNA complex structure. I'd like to use sequence file rather then molecular weight in the component definition of ASU. As there are solved homodimer protein structures (amino acid identity 100%) on PDB, I can download seq file (fasta form) from PDB webpage, but the seq file is only for one protein chain. I also tried online tools like "make sequence from PDB file" (http://swift.cmbi.ru.nl/servers/html/soupir.html), when I put the protein dimer bound to dsDNA pdb into the online tool, the outtput pir sequence file only shows a single protein chain and dna which dose not seems like two strands, rather then just put two 23base dna together for a 46 base length single strand DNA. I am asking is there a way to generate sequence file for a homodimer and dsDNA? or I have to generate sequence file for each chain separately (there will be four sequence files in this case, two protein chains and two dna chains)? Thanks. Alex Alex

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coot generate symmetry mates like pymol
by Xiao Lei 08 Jan '16

08 Jan '16

Hi Phenixbb members, 1. Is there a function in coot which can generate symmetry mates like pymol (action--> generate symmetry mates)? I know in coot there is a "Draw---> Cell&Symmetry" function, but it seems the display results could not display my crystal packing like pymol. 2. In pymol, is there a button which just display structure in one unit cell? Thanks. Xiao

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unwanted N/Q/H flipping in PHENIX.REFINE
by Bernhard Loll 05 Jan '16

05 Jan '16

Dear all, I am currently refining a 1.9 A structure with PHENIX 1.10.1-2155. The problem I am facing is the following: Running the Molprobity server, it suggests me to correct a couple of N/Q/H flips. I perform the flips re-run PHENIX.REFINE with “Automatically correct N/Q/H errors” not ticked. The log file confirms the selection with nqh_flips = False. Nevertheless PHENIX.REFINE again flips these residues and the output PDB file has all previously flipped residues “re-flipped” in comparison to the input PDB file. I am very confident that the automatically flips performed by PHENIX.REFINE (REDEUCE) are wrong, since I have two metal binding sites. Why PHENIX.REFINE rotates side chains by 180 degree even though nqh_flips were set to false? Any help is appreciated. Cheers, Bernhard Dr. Bernhard Loll Freie Universitaet Berlin Fachbereich Biologie, Chemie, Pharmazie Institut fuer Chemie und Biochemie AG Strukturbiochemie Takustr. 6 D-14195 Berlin Germany Phone: +49 (0) 30 838-57348 Fax: +49 (0) 30 838-454936 Email: loll(a)chemie.fu-berlin.de Homepage: http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/

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Project info lost after a disk crash
by hli 04 Jan '16

04 Jan '16

Hi, The hard drive of our major Linux computer crashed recently. After installing a new disk and recovering all the data in the damaged disk I lost all the project information in PHENIX GUI home page. I noticed that under .phenix directory there are files like project_db.pkl, but do not know how to retrieve the old project info into the GUI. Thanks in advance for your help. Huiying Dept. MB&B UC Irvine

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Re: [phenixbb] Modifications for Ca-binding site
by Nigel Moriarty 30 Dec '15

30 Dec '15

Jacob Once again Boaz is leading you in the correct direction. You did send me a *.metals.edits file. You just need to change the ideal distances in this file. On another point, I ran a refinement with your inputs and the values don't seem a long way off. However, I'd wait for Pavel to take a look because the density around the Calcium ion itself seems unusual. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Dec 30, 2015 at 6:27 AM, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > Hi Jacob, > > My guess is that answer (or hint) is here (taken from this link : > https://www.phenix-online.org/documentation/faqs/refine.html#targets-and-re…): > > > *I have ions very close to water molecules/protein atoms, and > phenix.refine keeps tring to move them apart. How can I prevent this?* > > Use phenix.ready_set or *phenix.metal_coordination* to generate custom > bond (and optionally, bond angle) restraints, which will be output to a > parameter file ending in ".edits". If you are using the PHENIX GUI, there > is a toolbar button for ReadySet in the phenix.refine interface, which will > automatically load the output files for use in phenix.refine. > > I have not used it myself but I assume that the sigmas for the restraints > would be in the *.edits files that you'll generate. > > Hope this helps. > > Boaz > > > > > > > > > > *Boaz Shaanan, Ph.D. Dept. of Life > Sciences Ben-Gurion University of the > Negev Beer-Sheva > 84105 > Israel > E-mail: > bshaanan(a)bgu.ac.il <bshaanan(a)bgu.ac.il> Phone: 972-8-647-2220 Skype: > boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 * > > > > > > ------------------------------ > *From:* Keller, Jacob [kellerj(a)janelia.hhmi.org] > *Sent:* Wednesday, December 30, 2015 4:09 PM > *To:* Nigel Moriarty > *Cc:* בעז שאנן; phenixbb(a)phenix-online.org > *Subject:* RE: [phenixbb] Modifications for Ca-binding site > > How does one change the ideal bond length/sigma in Phenix? > > > > JPK > > > > *From:* Nigel Moriarty [mailto:[email protected]] > *Sent:* Tuesday, December 29, 2015 10:12 AM > *To:* Keller, Jacob > *Cc:* Boaz Shaanan; phenixbb(a)phenix-online.org > *Subject:* Re: [phenixbb] Modifications for Ca-binding site > > > > Jacob > > > > Boaz has some sage advice. I recommend not excluding the Ca-O coordination > but changing the ideal to better reflect the distances in your files. > > > > PS I'd also like the PDB files, directly, so as not to put noise on the > list. > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Physical Biosciences Division > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > On Tue, Dec 29, 2015 at 5:49 AM, Keller, Jacob <kellerj(a)janelia.hhmi.org> > wrote: > > Well, I think it's more of a data-vs-geometry battle, with the geometry > dragging in the side chains towards the calciums, and the data pulling them > out. When I real-space refine them in Coot, some of the Ca-O distances are > pretty different from the "ideal" values. Maybe I could just exclude them > from xyz refinement in Phenix after making sure they're correct in Coot? > I'll give that a shot. > > Kol tuv, > > Jacob > > > > > > -----Original Message----- > From: Boaz Shaanan [mailto:[email protected]] > Sent: Tuesday, December 29, 2015 7:52 AM > To: Keller, Jacob; phenixbb(a)phenix-online.org > Subject: RE: Modifications for Ca-binding site > > Hi Jacob, > > Sucking-up neighboring residues into the Calcium (or other heavier atoms) > density is a known issue. Turning-off the Ca-O or other distance restraints > around the Calcium is the last thing you want to do, in my experience. > You'd better check those distance restraints and verify that they're > compatible with the distances in other (preferably high resolution, of > course) structures with calcium binding sites similar to yours and then > make sure they're given the appropriate weight during refinement. That's my > view but Pavel will give you more advices I'm sure. > > Cheers, > > Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > ________________________________________ > From: phenixbb-bounces(a)phenix-online.org [ > phenixbb-bounces(a)phenix-online.org] on behalf of Keller, Jacob [ > kellerj(a)janelia.hhmi.org] > Sent: Tuesday, December 29, 2015 4:44 AM > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] Modifications for Ca-binding site > > I am getting a lot of problems with my calcium binding sites--there is > clear density for the calciums and the protein side chains, but Phenix > keeps sucking the side chains out of their density towards the calciums and > also the calciums show some positive difference density, perhaps due to > too-high b-factors (or potentially partial occupancy by Na?). I think what > might work best is to turn off the Ca-O bond length restraints somehow, but > don't see where/how to do that. I tried releasing them from geometrical > restraints, but that made things worse, since things went haywire in the > sidechains themselves. > > Is it possible to make Phenix ignore the Ca-O bond distance restraints? > > JPK > > ******************************************* > Jacob Pearson Keller, PhD > Looger Lab/HHMI Janelia Research Campus > 19700 Helix Dr, Ashburn, VA 20147 > email: kellerj(a)janelia.hhmi.org > ******************************************* > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > >

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Modifications for Ca-binding site
by Keller, Jacob 30 Dec '15

30 Dec '15

I am getting a lot of problems with my calcium binding sites--there is clear density for the calciums and the protein side chains, but Phenix keeps sucking the side chains out of their density towards the calciums and also the calciums show some positive difference density, perhaps due to too-high b-factors (or potentially partial occupancy by Na?). I think what might work best is to turn off the Ca-O bond length restraints somehow, but don't see where/how to do that. I tried releasing them from geometrical restraints, but that made things worse, since things went haywire in the sidechains themselves. Is it possible to make Phenix ignore the Ca-O bond distance restraints? JPK ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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RSRZ in Phenix?
by Keller, Jacob 30 Dec '15

30 Dec '15

Dear Crystallographers, Is there any place in Phenix where RSRZ or a similar measure is shown? All the best, Jacob Keller ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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Coot add DNA base or mutate DNA base
by Xiao Lei 25 Dec '15

25 Dec '15

Hi All, I'm using coot to build DNA, when I click "add residue" to one end of DNA, coot automatically add an "A" base to it, but I'd like to add "G" base, is it a way to mutate the A base to G base, I know coot can mutate amino acid residue, is is a way to mutate DNA residue in coot GUI? Thanks ahead. Xiao

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Trouble refining following molecular replacement
by Tyler Liban 22 Dec '15

22 Dec '15

Hello all, We are currently working with a dataset for a trimeric protein complex at 3A that is giving us some issues. The space group seems to be P21 ( 59.5, 61.6, 99.6 , 90, 98, 90) and the Mathews coefficient (2.6) suggests 2 copies of this 35kDa complex in the ASU. We are using a homolog as the search model that is 80% identical, and Phaser is able to find 2 molecules in P21 when searching in the same point group and gives good TFZ scores (TFZ = 9 or 10). However, these solutions do not refine well following Phaser (Rfree ~.50), and after removing parts of the model that look incorrect the Rfree still stays between .46 and .50. We ran the data through Xtraige and saw no signs of twinning based on the L-test, and the Patterson map has one small off-origin peak that is only 5%, indicating that there is no significant pseudotranslation. We have also tried finding MR solutions in P1, but haven’t had much luck. Any ideas on where to go from here would be greatly appreciated. Tyler

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command line for reflection file editor
by Zheng Zhou 22 Dec '15

22 Dec '15

Dear phenix experts, How do I combine Rfree from one dataset with the new dataset under command line? I can do this using reflect file editor GUI easily. But I tried to look up the documentation for phenix.reflection_file_converter and could not find a solution. I am trying to write a script to handle several datasets scaled from HKL2000. I could do this easily in ccp4, but looks like Ctruncate's French&Wilson made the completeness worse than scale.log. Thanks for your help in advance. Best, Zheng

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mmCIF file must contain at least one data block
by Ursula Schulze-Gahmen 18 Dec '15

18 Dec '15

I am getting this thie error message mmCIF file must contain at least one data block when trying to run readyset or phenixrefine I cannot find anything wrong wqith my input files. What is the problem? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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remove old phenix version but keep the processed data
by Xiao Lei 17 Dec '15

17 Dec '15

Hi Phenixbb member, As I updated Phenix version on my Macbook pro (OS X 10.10), I found the newer version phenix did not automatically replace the old versions. Is there a way to remove the old version Phenix safely and only keep the newer version, but at the same time keep the processed data (data from phenix refine and xtriage)? Thanks ahead. Xiao

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ML with Twinning?
by Keller, Jacob 16 Dec '15

16 Dec '15

Is Phenix able yet to use the ML target function with twinned data? Is it in the works? All the best, Jacob Keller ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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differences in refinement stats between phenix-dev-2219 and -1.9-1692
by Ezequiel Noguera 16 Dec '15

16 Dec '15

Thank you very much, Pavel. I don't save H's when I modify the model in coot (the input PDB file that I sent you was the output from coot). I did the refinement again, now in version 2247, without NCS. I got the same results, higher R factors and RMS deviations for the newer version. I got better results when I used "update waters" (both in Rfactors and RMS). Below, I list the statistics for refinement without updating waters. Significant differences remain. Could it be any difference in settings of default parameters between versions? version: dev-2247 Start: r_work = 0.1687 r_free = 0.2011 bonds = 0.046 angles = 1.321 Final: r_work = 0.1753 r_free = 0.2040 bonds = 0.030 angles = 0.593 version: 1.9-1692 Start: r_work = 0.1651 r_free = 0.2018 bonds = 0.013 angles = 1.409 Final: r_work = 0.1663 r_free = 0.2017 bonds = 0.011 angles = 1.321

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Re: [phenixbb] -differences in refinement stats between phenix-dev-2219 and -1.9-1692
by Pavel Afonine 13 Dec '15

13 Dec '15

Hi Ezequiel, just to make it clear: torsion-angle NCS, Optimize X-ray/stereo weight are *not* the default settings, therefore you did customize the refinement parameters. At this resolution (1.3A) you do not need to use NCS restraints. Also, you say you used "Automatically add H's" however the PDB file you sent me does not contain any H atoms. Furthermore, the PDB file header says H are present: REMARK MODEL CONTENT. REMARK ELEMENT ATOM RECORD COUNT OCCUPANCY SUM REMARK C 1275 1047.00 *REMARK H 2029 1649.00 * REMARK O 559 488.50 REMARK N 315 263.00 REMARK S 6 6.00 REMARK Cu 4 2.89 REMARK TOTAL 4188 3456.39 So overall this make an impression that something has gone wrong. Way forward: 1) Take the file you sent me; 2) Add H atoms: phenix.reduce model_no_h.pdb > model_with_h.pdb 3) Use new file with H atoms added to run refinement. The only setting different from defaults should be "Optimize X-ray/stereo weight". Perhaps you can also enable automated water update. I just did all this myself and got nicely refined model with Final: r_work = 0.1624 r_free = 0.1939 bonds = 0.010 angles = 1.030 Corresponding PDB and MTZ are sent in a separate email that goes to you only (off mailing list). Pavel On 12/6/15 07:59, Ezequiel Noguera wrote: > Hi Pavel, thank you very much for your help. I attach the data. I > didn´t customize parameters. The refinement stategy of the last job > was: XYZ coords, Real-space, Individual B-factors, torsion-angle NCS, > Optimize X-ray/stereo wght and X-ray/ADP wght, Automatically add H's > and correct N/Q/H errors. > > > Hi Ezequiel, > > deviations are not unexpected in general but not that large as you > report, so I wonder what's going on.. Could you please send me input > data and model files, as well as any ligand files you used. If you > customized some parameters, telling what were those would be helpful too. > > Please send all files off-list to my email directly. > > Thanks, > Pavel > > >> Hello, I'm working in a refinement that I started some time ago. I >> noted that repeating the same refinement task using a newer version >> of phenix, the refinement statistics Before and After refinement are >> different from values of the old version (I used "restore job" from >> the Job history to repeat the same task in the two versions installed >> in the same PC). Any explanation? I'm worried about the rms >> deviation. Thanks in advance. >> >> new version: >> R-work: start=0.1697, final=0.1761 >> R-free: start=0.2011, final=0.2053 >> Bonds: start=0.046, final=0.029 >> Angles: start=1.321, final= 0.631 >> >> old version: >> R-work: start=0.1651, final=0.1657 >> R-free: start=0.2018, final=0.2009 >> Bonds: start=0.013, final=0.013 >> Angles: start=1.409, final= 1.411

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autosolve density modification question
by Scott Horowitz 10 Dec '15

10 Dec '15

Hi, a quick question: if when running autosolve on SAD data, if I set the parameter build = false, will that disable all model building, including any model building that would be a part of the density modification process? I'm especially curious about the case if build = false, but mask_type = histograms. I am currently assuming that the histogram matching does not use model building as part of it, and would like to know if this interpretation is correct. 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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Phenix dev-2247 fails to start
by Chen Zhao 07 Dec '15

07 Dec '15

Dear developers, I am now having some troubles initiating the most updated nightly built dev-2247. I have to use this version because it is supposed to have a bug fixed based on my bug report in November. My machine is running Debian 7 with kernel version 3.2.0-4-amd64. And the pheinx installation file I downloaded is the 64 bit linux version for CentOS 5. The symptom is that after I called phenix from a terminal window, there is an error message saying "local 'en_GB' cannot be set" (which is always the case and which does not seem to matter). After that, phenix GUI did not start at all, but ps command shows two python2.7 processes running. Running phenix from command line seems to work fine. Before switching to this version I was running the stable version 1.10.1-2155, and have no problem. Is there any simple fix? If not, I will probably just stick to the command line version for the moment. Thanks a lot, Chen

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differences in refinement stats between phenix-dev-2219 and -1.9-1692
by Ezequiel Noguera 06 Dec '15

06 Dec '15

Hello, I'm working in a refinement that I started some time ago. I noted that repeating the same refinement task using a newer version of phenix, the refinement statistics Before and After refinement are different from values of the old version (I used "restore job" from the Job history to repeat the same task in the two versions installed in the same PC). Any explanation? I'm worried about the rms deviation. Thanks in advance. new version:R-work: start=0.1697, final=0.1761R-free: start=0.2011, final=0.2053Bonds: start=0.046, final=0.029Angles: start=1.321, final= 0.631 old version:R-work: start=0.1651, final=0.1657R-free: start=0.2018, final=0.2009Bonds: start=0.013, final=0.013Angles: start=1.409, final= 1.411

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Trends In Initial Crystallization Screening (Reminder)
by Mustafa Koksal 30 Nov '15

30 Nov '15

Dear members of the crystallography community, I would like to assess the tendency/trend in our community to outsource initial crystallization screening experiments. Here, outsourcing refers to sending your protein/DNA/RNA sample to a service provider, who will set up crystallization experiments, take images of crystallization drops at various time points, make images available to you, and, if you require, send you the plate to retrieve any crystals. To do assessment, I prepared a short-answer questionnaire, which contains 10 questions and should take less than 5 minutes to complete. I especially encourage the new PIs and young researchers to complete the questionnaire. Could you please fill out the questionnaire at the following link? https://tr.surveymonkey.com/r/BVNCPVV In case you are unwilling to click links in e-mails, I also included the questions here. Please reply with answers in private to: mustafakoksal(a)iyte.edu.tr Thank you very much for your contribution. Mustafa Questionnaire: 1. Have you outsourced initial crystallization screening experiments in any of your projects before? Yes No 2. If you did, what format and type of experiment you used (choose all that apply)? 96 well/plate 384 well/plate 1536 well/plate Sitting Drop Hanging Drop Microbatch Other (please specify) 3. If you did, what price did you pay per 96-conditions? 4. If you did not, what prevented you from outsourcing (choose all that apply)? It is costly Shipping a sample is hard Privacy concerns I prefer to do it in my lab I do not think it is advantageous I do not have enough sample Other (please specify) 5. Would you be interested in outsourcing initial crystallization screening experiments in future? Yes No 6. If you are interested, which method would you prefer (choose all that apply)? Sitting Drop Hanging Drop Microbatch Counter Diffusion Other (please specify) 7. If you are interested, up to what price would you be willing to pay per 96-conditions? $1 $2 $3 $4 $5 $6 $8 $10 $12 $15 $20 $25 $30 $50 8. If you are interested, what would be your minimum-maximum throughput (# of 96-condition experiments per month)? Note: a 1536-condition experiment is 16 x 96-condition experiments? 1 - 2 2 - 4 4 - 8 8 - 12 12 - 16 16 - 32 32 - 64 32 - 128 More than 128 9. How much sample would you be willing to sacrifice per screening 96-conditions (please specify in micrometers)? 10. Do you have any other comments? End of Questions -- Mustafa Koksal Postdoctoral Fellow University of Pennsylvania Department of Chemistry Roy and Diana Vagelos Laboratories Office: 2090 IAST Office Phone: (215) 898-2227 Mobile Phone: (267) 319-6443 Mail Address: 231 S. 34th St, Philadelphia 19104, USA --

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lose the jobs history when update/install phenix new version
by caio reis 26 Nov '15

26 Nov '15

Hi, my name is Caio, I do Ph.D in biomolecular physics at University of Sao Paulo, Brazil, and I am writing to know if anyone knows if I'm gonna lose my job history in Phenix, if I update my version to the newest one. I work with many proteins and structures (MR, autobuild, phenix.refine, etc), so as I can better manage my jobs and archives using and consulting my job history in Phenix interface. I also want to know, if I can use de openmp without having to compile phenix again...because I don't want to lose my job history (in case it can be lost when Phenix is updated/installed again/compiled). Thank you in advance.

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RapiData 2016
by Smith, Clyde 26 Nov '15

26 Nov '15

The 2016 RapiData Course on Data Collection and Structure Solution will take place at the Stanford Synchrotron Radiation Lightsource (SSRL) from April 24-29 2016. 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://smb.slac.stanford.edu/rapidata-2016/about.html The deadline for applications is January 4th 2016. To apply follow this link: http://smb.slac.stanford.edu/rapidata-2016/registration.html 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 without restrictions on a per need basis. The instructions to apply for these scholarships can be found in the application page. RapiData 2016 will take place immediately after Crystallization: Focus on Micro and Nano Crystals and High Throughput Methods (April 19-22 2016), also at SSRL. Together, the two courses will cover most aspects of crystal structure determination and we encourage participation in both. For information about the Crystallization course see http://smb.slac.stanford.edu/news/cryst_focus_on/cryst_focus_on_2016/ or contact the organizers: Vivian Stojanoff (vivian.stojanoff(a)gmail.com) or Silvia Russi (srussi(a)slac.stanford.edu) The Organizing Committee of RapiData 2016 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

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error when running phenix_rosetta_refine
by Wei Wang 19 Nov '15

19 Nov '15

Hi, I just experienced an error when using phenix_rosetta_refine. It appeared after "Generating 5 models". I'd appreciate any help on solving this. Generating 5 models on 3 processors... DEBUG dumping error message ERROR: Rosetta exited with status 1 stderr output: Traceback (most recent call last): File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/rosetta/xray_target.py", line 203, in compute_target tfx_r = self.target_functor(compute_gradients=compute_gradients) File "/Applications/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/targets.py", line 247, in __call__ compute_gradients=compute_gradients)) File "/Applications/phenix-1.10.1-2155/modules/cctbx_project/cctbx/xray/target_functors.py", line 58, in __call__ compute_gradients=compute_gradients) RuntimeError: cctbx Internal Error: /Users/builder/slave/phenix-nightly-mac-intel-osx-x86_64-10_9/modules/cctbx_project/cctbx/xray/targets.h(498): CCTBX_ASSERT(f_calc.size() == f_obs.size()) failure. ERROR: error computing X-ray target

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Re: [phenixbb] (no subject)
by Ashok Nayak 19 Nov '15

19 Nov '15

Dear luzuok, The merging job can easily be done in Pymol. 1.Create symmetry molecules (say at 4A radius) -> Select the symmetry related molecules of your choice -> save the selected coordinates of the same or 2.You can also do the same by saving the coordinates of two symmetry related molecules separately and merge in a text file with proper TER records. regards Ashok CSIR-CDRI Lucknow, INDIA On Wed, Nov 18, 2015 at 9:09 PM, Ashok Nayak <ashokgocrackin(a)gmail.com> wrote: > Dear luzuok, > The merging job can easily be done in Pymol. > 1.Create symmetry molecules (say at 4A radius) -> Select the symmetry > related molecules of your choice -> save the selected coordinates of the > same > or > 2.You can also do the same by saving the coordinates of two symmetry > related molecules separately and merge in a text file with proper TER > records. > > regards > Ashok > CSIR-CDRI > Lucknow, INDIA > > On Wed, Nov 18, 2015 at 5:59 PM, luzuok <luzuokun(a)126.com> wrote: > >> Dear Tom, >> I have the same question too. >> Another simple question is that how can I merge two symmetry related >> molecule? Though I can easily expand them by coot. >> >> Best! >> Lu >> >> >> -- >> >> >> Lu Zuokun, Ph.D. Candidate >> College of Life Science, Nankai University >> >> 在 2015-11-18 23:14:48，"Terwilliger, Thomas Charles" <terwilliger(a)lanl.gov> >> 写道： >> >> Hi Ashok, >> >> If you have a PDB file with 2 crystallographically-related copies of your >> molecule, with one called chain A and one called chain B, you can run >> phenix.simple_ncs_from_pdb on your PDB file to find the matrices and >> translations. Let me know if that doesn't do it! >> >> All the best, >> >> Tom T >> >> >> ------------------------------ >> *From:* phenixbb-bounces(a)phenix-online.org < >> phenixbb-bounces(a)phenix-online.org> on behalf of Ashok Nayak < >> ashokgocrackin(a)gmail.com> >> *Sent:* Wednesday, November 18, 2015 7:58 AM >> *To:* phenixbb(a)phenix-online.org >> *Subject:* [phenixbb] (no subject) >> >> Hello Phenix BB, >> Like every amateur crystallographer I could easily generate symmetry >> mates in a given radius in coot, but I wondered always which is the >> crystallographic two fold axis axis(my space group being C2) through which >> the molecule is rotated and translated (if it is) to get the next molecule. >> I tried superpose to find the answer, but could only get the Euler angles >> and transformation matrix and not the axis. Are there any programs where I >> can get to know this, would be grateful to be enlightened for the same >> >> thanks BB in advance >> >> >> >> regards >> >> -- >> Ashok Nayak >> PhD student- >> Molecular and Structural Biology Division >> CSIR-CDRI, Janakipuram Extension >> Lucknow-226031 >> India >> >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > > > -- > Ashok > Senior Research Fellow - Dr JV Pratap, Lab No-LSN 008 > Molecular and Structural Biology Division > Central Drug Research Institute, Janakipuram Extension > Lucknow-226031 > India > -- Ashok Senior Research Fellow - Dr JV Pratap, Lab No-LSN 008 Molecular and Structural Biology Division Central Drug Research Institute, Janakipuram Extension Lucknow-226031 India

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(no subject)
by Ashok Nayak 19 Nov '15

19 Nov '15

Hello Phenix BB, Like every amateur crystallographer I could easily generate symmetry mates in a given radius in coot, but I wondered always which is the crystallographic two fold axis axis(my space group being C2) through which the molecule is rotated and translated (if it is) to get the next molecule. I tried superpose to find the answer, but could only get the Euler angles and transformation matrix and not the axis. Are there any programs where I can get to know this, would be grateful to be enlightened for the same thanks BB in advance regards -- Ashok Nayak PhD student- Molecular and Structural Biology Division CSIR-CDRI, Janakipuram Extension Lucknow-226031 India

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phenix 1.10.1-2155 has no kicked map option
by Tarek DawoD 18 Nov '15

18 Nov '15

Dear Phenix developer why i could not see the kick map option under phenix.refine (GUI). i used to use it in the previous version. Kick in phenix 1.9.1692 no Kick in phenix 1.10.1-2155 Best RegardsTDawoD

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Re: [phenixbb] Omit map output map files
by Fischmann, Thierry 17 Nov '15

17 Nov '15

What Pavel describes is how to get a “difference map”. But it is not an “omit map” per the original definition. The omitted part should never have been part of the model during any refinement step before the omit map is calculated. The purpose is to prevent bias. If the model has already been refined with a ligand, then the technique of simulated annealing refinement can be used to remove the bias after removing the ligand. This approximates an “omit map” (still one may argue not a real “omit map”, but close enough). Thierry From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Manoj saxena Sent: Sunday, November 15, 2015 11:20 PM To: Pavel Afonine Cc: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Omit map output map files Thanks Dr. Pavel, This looks simple. regards Manoj On Sun, Nov 15, 2015 at 11:49 PM, Pavel Afonine <pafonine(a)lbl.gov<mailto:[email protected]>> wrote: Hi Manoj, you can do it this way: 1) remove ligand from PDB file; 2) compute mFo-DFc map. This is your ligand-omit map. Some would advise to do a round of refinement between steps 1-2 above in order to remove "memory from the ligand". I'm not convinced this is critical though. Pavel On 11/15/15 12:18, Manoj saxena wrote: Greetings, I would be very grateful if someone can help me to explain in I can get F0-Fc omit maps of a particular ligands using Phenix. I am trying to generate an omit map for the ligands in my protein model using the composite omit map GUI feature of phenix version 1.10.1-2155. I selected my ligands by using atom selection feature under the map options(and in the omit map method I put refine). What map type I should give in the map types input to get the F0-Fc maps. Currently I may getting a map that look like my 2F0-Fc map that I got after my refinement. Also, I have no waters in my model. Can we define areas (boxes) around the ligand to generate omit map of that particular region to get output maps with densities like Fo-Fc maps. So many thanks in advance. Regards Manoj Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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Omit map output map files
by Manoj saxena 16 Nov '15

16 Nov '15

Greetings, I would be very grateful if someone can help me to explain in I can get F0-Fc omit maps of a particular ligands using Phenix. I am trying to generate an omit map for the ligands in my protein model using the composite omit map GUI feature of phenix version 1.10.1-2155. I selected my ligands by using atom selection feature under the map options(and in the omit map method I put refine). What map type I should give in the map types input to get the F0-Fc maps. Currently I may getting a map that look like my 2F0-Fc map that I got after my refinement. Also, I have no waters in my model. Can we define areas (boxes) around the ligand to generate omit map of that particular region to get output maps with densities like Fo-Fc maps. So many thanks in advance. Regards Manoj

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Re: [phenixbb] [ccp4bb] question on mtz file
by Smith Lee 15 Nov '15

15 Nov '15

Dear Ian, The mtz was transformed from a cryo-EM mrc file by phenix.map_to_structure_factors, and it contains both label "F" and "F_ampl". When I do phenix.mtz.dump, the labels include H,K,L,F,PHIF,F_ampl,HLA,HLB,HLC,HLD. Smith On Sunday, November 15, 2015 11:03 PM, Ian Tickle <ianjt05(a)gmail.com> wrote: Hi, I assume what you mean is "what is the difference between the column labelled 'F' and the one labelled 'F_ampl' ?" in your MTZ file. Since MTZ column labels are effectively arbitrary and may be user-specified, that is clearly an impossible question to answer without knowing the history of your MTZ file. The column labelled 'SIGFP' would normally be the standard deviation of the 'FP' column (assuming there is such a column), though there's no absolute requirement that this be the case (it just makes life easier for everyone if it is!), so again it's impossible to say which amplitude column the SIGFP column is related to without knowing the history of your file. Bottom line is: you have not supplied sufficient information to make it possible to answer your question. Cheers -- Ian On 15 November 2015 at 02:27, Smith Lee <00000459ef8548d5-dmarc-request(a)jiscmail.ac.uk> wrote: Dear All, For a mtz file, will you please introduce to me the difference between label "F" and label "F_ampl"? For the label "SIGFP", is it the deviation related to label "F" or label "F_ampl"? Smith

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ionic radius
by Manoj saxena 13 Nov '15

13 Nov '15

Greetings, I was wondering if someone can enlighten me on the issue of how the metal ionic radius are defined in the protein structures. Is there any place in the refinement process where we can define it or it is automatically taken from some library in the phenix background. What is a good resource for knowing the ionic radii, I came across this one in an old blog post http://abulafia.mt.ic.ac.uk/shannon/ is there any other source that is used. Thanks so much in advance Manoj Saxena

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Rigid body refinement
by Rex Palmer 12 Nov '15

12 Nov '15

We have 1.5A resolution data for a heterodimeric protein with linked A and B chains. Phenix MR has produced a promising solution. We would now like to perform an initial refinement using Phenix with the A chain and B chain individually treated as rigid bodies.Is this possible with Phenix and if so how? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://www.springer.com/978-1-4614-3954-7

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