- phenixbb - phenix-online.org

Autobuild error
by Lau Sze Yi (SIgN) 08 Apr '15

08 Apr '15

Hi, I did an Autobuild run. The Status panel indicated that the run is finished. In the Model building panel the status of run# 5 still says running (See attached screenshot). Is this normal? And when I click on run #4 to Open in Coot, I get an error message indicating that the directory could not be found (see attachment). What is wrong and how can I fix this? I am using version phenix-1.9-1692 on Mac. Regards, Sze Yi Research Fellow Singapore Immunology Network (SigN) 8A Biomedical Grove, #03-06 Immunos, Singapore 138648 DID: +65 6407 0640 Fax: +65 6407 0640

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on reciprocal space refine of the electronic microscopy map by Phenix
by Smith Liu 08 Apr '15

08 Apr '15

Dear All, Recently there are cryo-electronic microscopy papers which refine the reciprocal space of the electronic mcroscopy map by phenix refine. For the electronic mcroscopy map, what does it mean for the reciprocal space? How to get the reciprocal space map from the electronic mcroscopy map? In order to realize this kind of refine in phenx, we only process the xyz coordinates strategy refine in the graphical interface, right? I am looking forward to getting your reply. Smith

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FINAL REMINDER: Neutrons in Structural Biology
by Meilleur, Flora 06 Apr '15

06 Apr '15

6th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 1 - June 5, 2015 Application deadline: April 10, 2015 Detailed information can be found on the workshop web page: https://public.ornl.gov/neutrons/conf/gcnb2015. Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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Ensemble refinement
by mohamed noor 04 Apr '15

04 Apr '15

Using the FEM map, I managed to remove more bad waters and add instead ions from the crystallization mix. I tried phenix.ensemble_refinement but the Rfactor increased by 2 % (originally 19/22 % from phenix.refine). Before it crashes at the validation point all the time, it prints out the validation summary with 0.53-3.48 % and 1.87-7.22 % Ramachandran outlier (from 0.3 %, supported by density) and a Molprobity score of 1.57-1.92 and 1.82-2.14 depending on pTLS used (original single model score was 2.08). The clashscore in both settings (pTLS=0.6 and 1) are 0. Do I still go by the Rfactor and decide to not use ensemble refinement at all? Thanks.

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Structure with pseudo-NCS translation
by Mark A Saper 03 Apr '15

03 Apr '15

I know that Phaser takes account of NCS translation in the likelihood statistics ( Read, Adams, McCoy (2013) Intensity statistics in the presence of translational non crystallographic symmetry”). Has this also been incorporated into phenix.refine? I have a structure with pseudo NCS translations because of NCS rotational symmetry. One suggestion that I found in the archives, was to explicitly LS target refinement rather than ML. Any comments? Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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refinement
by Almudena Ponce Salvatierra 02 Apr '15

02 Apr '15

Dear all, I am using Phenix.refine after MR and I have a complete model and data to 2.8 Angstrom resolution. However, for some reason, Phenix does not place any water molecules. Is there a setting I could change in order to see whether this situation changes? What could the reason be? Thanks a lot in advance. Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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twinning
by Shun Liu 01 Apr '15

01 Apr '15

Dear all, Recently I have got a data set that diffracts to 1.7 angstrom. Images look good. During data processing I did not find anything that looks strange. However, when I was doing Phaser-MR, I got a warning: “ Intensity moments suggest significant twinning (>5%). Tests based on possible twin laws will be more definitive.” What does this mean? A twinning data set? I still found a solution and refined the model step by step, using the data (20-1.7 angstrom). It seems that the final model and map are acceptable. But R-factors are 0.24/0.28, very high. Does the twin cause the high R-factors? Is there a solution to detwin? Or are the R-factors acceptable for a twinning data set? Any suggestions are appreciated and thanks in advance! Best, Shun

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a question on henix refine
by Smith Liu 01 Apr '15

01 Apr '15

Dear All, For the Phenix refine, the default for the Scattering table in "other options" in the graphical interface is n_gaussian, in which situation to use electron is much better? And how much would be the benefit to use electron instead of n_gaussian? Smith

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Maps
by mohamed noor 01 Apr '15

01 Apr '15

Dear developers What is the difference between MEM and FEM maps? I read the documentation and my understanding is both are supposed to create beautiful maps :) My problem is I have a structure at 1.9 A (a different protein than the one referred to in my previous question), the Rfactor is around 20/22 %, Rms bonds is 0.03 and Rms angles is 1.845. If the bonds/angles get lower, the Rfactor jumps up (same problem as the other structure). Looking in Coot, there are positive and negative density and missing density for the side chains of residues with high B factor. For some reason, phenix.refine keeps on adding water at strange places even at regions that I suspect to be just noise. For this reason, I want to see if the noise is really noise. A second reason is I have density that seem to be too big for a water molecule but waters were placed anyway, so I want to know if these are real positive density. The dataset was obtained from only 50 degrees, SG is P 61 2 2. Including more images brought up the Rmerge to 30-40% and Rfactor being stuck at 30 %. For some reason, I don't find the X-ray statistics from the phenix.model_vs_data logfile but in essence, I have: 28-1.9: 82 % 6 A - infinity: 95 % in the shells (2.25-2.14, 2.14-2.04, 2.04-1.97, 1.97-1.9) my completeness is around 85-62 % and CCwork is at least 70 % and CC1/2 of the dataset is 60 % at the highest resolution shell. Thanks.

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continuously Rfree lower than Rwork
by Smith Liu 31 Mar '15

31 Mar '15

Dear All, If in a Phenix.refine proces, the Rfree continuously lower than Rwork, what does it mean? Smith

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Twinning
by Shun Liu 31 Mar '15

31 Mar '15

Dear all, Recently I have got a data set that diffracts to 1.7 angstrom. Images look good. During data processing I did not find anything that looks strange. However, when I was doing Phaser-MR, I got a warning: “ Intensity moments suggest significant twinning (>5%). Tests based on possible twin laws will be more definitive.” What does this mean? A twin data set? I still found a solution and refined the model step by step, using the data (20-1.7 angstrom). It seems that the final model and map are acceptable. But R-factors are 0.24/0.28, a little high. Does the twin cause the high R-factors? Is there a solution to detwin? Or are the R-factors acceptable for a twin data set? Any suggestions are appreciated and thanks in advance! Best, Shun

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First-Science Discussions for Life-Science Beamlines at NSLS-II: April 21-22, 2015
by Robert Sweet 27 Mar '15

27 Mar '15

We will hold a "First Science at the ABBIX Beamlines" meeting on Tuesday - Wednesday, April 21-22, 2015, pertaining to the National Institutes of Health (NIH)-sponsored "Advanced Beamlines for Biological Investigations with X-rays" (ABBIX) Project. These three state-of-the-art beamlines are now under construction at the National Synchrotron Light Source (NSLS)-II facility at Brookhaven National Laboratory (BNL). Two of the beamlines are for macromolecular crystallography (MX), and the third is for life sciences applications of x-ray scattering. Visit this web site for further information and registration materials: http://workshops.ps.bnl.gov/?w=ABBIXApr2015 Briefly, the MX beamline called FMX - Frontier MX - is optimized to address microbeam applications, and the other called AMX - Highly Automated MX - is optimized for highly automated throughput. The scattering beamline called LIX - High Brightness X-Ray Scattering for Life Sciences - will offer multiple modes of study. The MX beamlines view canted undulator sources, and the scattering beamline views a single undulator, providing world-leading brightness. Current plans are to conclude construction by the end of 2015 and start commissioning then. During the commissioning period, opportunities will arise to perform early experiments before the general user programs of the beamlines commence in 2016, and it is the upcoming meeting's purpose to explore and discuss scientific areas and opportunities on which early operation of the beamlines could capitalize. Note: Registration is required. There is no registration fee. Visit this site to register: http://workshops.ps.bnl.gov/?w=ABBIXApr2015 Those who registered for the original meeting planned for January must re-register for the new occurrence in April. Contributed presentations describing experiments that exploit the capabilities of the ABBIX beamlines will be selected from submitted abstracts. The meeting will consist of both plenary and parallel sessions. The plenary session will begin with presentations on science topics in research fields that the beamlines are designed to address, followed by facility presentations to update the community about the early scientific capabilities at the suite of ABBIX beamlines and, in addition, of the Life Science and Biomedical Technology Research Resource (LSBR), sponsored by the NIH and the Department of Energy Office of Biological and Environmental Research (DOE BER). Two parallel sessions on Tuesday afternoon will focus on MX and x-ray scattering, consisting mainly of presentations that will address specific opportunities in these areas. These will be followed by two more parallel sessions on Wednesday morning, also focusing on MX and x-ray scattering, which will include contributions. If you wish to give a contributed presentation during one of the parallel sessions, please submit an abstract here: http://workshops.ps.bnl.gov/abstracts/default.aspx?w=ABBIXApr2015 The parallel sessions are designed to provide forums to facilitate more detailed discussions about potential first experiments at specific beamlines and the formation of the experiment teams. Specifically, each parallel session group will be charged to accomplish these goals: 1. Identify key research projects and the associated first experiments that may be performed at the suite of ABBIX beamlines, emphasizing those projects that will take advantage of NSLS-II properties and ABBIX beamline capabilities. 2. Facilitate the formation of research teams to generate first experiment proposals for submission. 3. Identify key additional team members in such areas as theory and analysis, ancillary measurements, and specimen preparation, needed to achieve the research goals. Confirmed invited speakers: Karen Allen (Boston Univ), Martin Caffrey (Trinity College Dublin), Seth Darst (Rockefeller Univ), Richard Gillilan (Cornell Univ), Wayne Hendrickson (Columbia Univ), AndrHoelz (California Inst Tech), Huey Huang (Rice Univ), Shenping Liu (Pfizer), Lee Makowski (Northeastern Univ), David Ostrov (Univ of Florida), Rebecca Page (Brown Univ), Anna Marie Pyle (Yale Univ), Christian Riekel (ESRF), Thomas Schneider (EMBL-Hamburg), John Tainer (Scripps Research Inst). We would like two outcomes from this meeting: (a) a concise meeting report outlining how ABBIX beamlines will help to address outstanding problems in life sciences, and (b) a list of potential first experiments along with the corresponding research teams. For more information on the meeting, please contact Sonya Kiss, at skiss(a)bnl.gov. Note: Registration deadline is Tuesday, April 14, 2015. Organizers: Lonny Berman ABBIX Project Manager National Synchrotron Light Source II Brookhaven National Laboratory Sean McSweeney Structural Biology Program Manager Photon Sciences Division Deputy Director National Synchrotron Light Source II

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can mr_rosetta include twin_law?
by Ni, Fengyun 27 Mar '15

27 Mar '15

Hi everyone, When I run phenix.mr_rosetta, I use the following file (twin.eff) to add the twin_law with the keyword: refinement_params=twin.eff. I checked the output that the phenix.refine stage could recognize this file. But the autobuild step can not read this file and give the error information as follows, refinement.twinning { twin_law = "h,-h-k,-l" } Unable to read the parameters file twin.eff. Is there anyway to overcome this issue? Thank you very much in advance! Fengyun

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Refinement
by mohamed noor 26 Mar '15

26 Mar '15

Dear all I have a structure at 1.4 A currently with an Rfactor of 21/26 %. I notice from the plot by cycle that everytime the RMS bonds/angles reduce, the Rfactor increases a few percent. Is there any way of telling phenix.refine to not 'restrain' the model too much? I have already used automatic weighting. Also, RINGER identified a few alternate conformations, so I'm thinking that modeling this might account for a better model. However, as I have an NCS of 4, this can be tedious to do by hand, and AFAIK, phenix.refine does not create new conformations. Is there an alternative? Final question, some residues were flagged as having high B factors but not in all the copies. How do I deal with this? Some background: I initially had problems with refinement being stuck at 30-35 % in SG P 3 2 1 (as suggested by Pointless and Xtriage). However, the beamline scientist suggested that there could've been lattice translocation and that it is actually P 3. Reintegrating seems to have solved the problem. With integrated data up to 1.2 A, I tried cut-off at 1.4, 1.3 and 1.2 A. Together with CC1/2 and refinement results, I chose 1.4 A, but should I cut it a bit lower? Thanks.

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PhD position in Structural Biology in Norway
by Hans-Petter Hersleth 24 Mar '15

24 Mar '15

Dear all, A 3- or 4-year PhD position in Structural Biology / Biophysics / Biochemistry starting August 2015 is available at University of Oslo, Department of Biosciences, Section for Biochemistry and Molecular Biology in the Metalloprotein group. The project is in the field of structural biology, biophysics and biochemistry with an emphasis on protein crystallography and spectroscopy (UV-vis, Raman and EPR) in combination with other biochemical and biophysical methods. The project is dealing with different redox proteins involved in oxygen activation and electron transfer. The focus will be on some enzyme systems like ribonucleotide reductase and nitric oxide synthase, their reaction mechanism and redox activation pathways. More information about the project, position and application procedure is found on the website: http://uio.easycruit.com/vacancy/1352831/96323?iso=no Applicants must hold a Master's degree or equivalent in structural biology, bioinorganic chemistry, biochemistry, biophysics, protein crystallography or related fields. We are seeking a highly motivated candidate that should have skills and experience in working with proteins or bioinorganic molecules. It would be advantageous with hands-on experience within topics like cloning, protein expression, purification, crystallisation, protein crystallography, spectroscopy, bioinorganic chemistry, protein-protein interactions, enzyme kinetics and redox-, radical- and metalloproteins. Candiates without a Master's Degree have until 30 June 2015 to complete the final exam. Application deadline is 13th April 2015 through the website: http://uio.easycruit.com/vacancy/1352831/96323?iso=no For further information please contact: Dr. Hans-Petter Hersleth, (h.p.hersleth(a)ibv.uio.no) ---------------------------------------------------------------------------------------------- Hans-Petter Hersleth, PhD Project Leader, Researcher and Senior Lecturer Department of Biosciences, University of Oslo Section for Biochemistry and Molecular Biology P.O.Box 1066 Blindern, NO-0316 Oslo, Norway Phone: +47 2285 4631 Fax: +47 2285 4726 Mobile: +47 413 33 126 http://www.hersleth.org/ -----------------------------------------------------------------------------------------------

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on Phenix's "Generate "Table 1" for journal"
by Smith Liu 23 Mar '15

23 Mar '15

Dear All, With the Phenix refine PDB and mtz file, I just prepared a "Table 1" for journal with Phenix. Here I find something special, which I hope I can get your advice. First, for the "Total reflections" and "Multiplicity", they are empty (no data given). Wil you please tell me why? Secondly, it writes, "Statistics for the highest-resolution shell are shown in parentheses". Suppose my crystal resolution is 2.5-45.6, then the the highest-resolution value should be 2.5, rather than 45.6, right? In addition, what is the diffrence between highest-resolution shell in the Table 1 and highest-resolution bin in the "Results" of Phenix refine? What is R-merge, R-meas,CC1/2 and CC*? I can get these data from MOSFLM output mtz file. But is my images were processe by HKL, which I have no experience, then how can I get the R-merge, R-meas,CC1/2 and CC*? I am looking forward to getting your reply. Smith

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question related to phenix produced PDB file
by Dialing Pretty 22 Mar '15

22 Mar '15

Dear All, In my Phenix refine produced PDB file, I find in REMARK 3, there is a sentence "PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED): 42.3. Does 42.3 means 42.3%? Is it too high? I am looking forward to getting your reply. Dialing

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error message in phenix refine
by Almudena Ponce Salvatierra 20 Mar '15

20 Mar '15

Hi everyone, I have merged 3 mtz files into one and done successfully Molecular replacement with it. However when I try to refine, I get the following error message: "cctbx error: merge_equivalents_exact: imcompatible flags for hkl (0, 0, 16) (mismatch between Friedel pairs). How can I fix this? Thank you very much in advance. Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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fixing rotamers with coot
by Benoît Masquida 19 Mar '15

19 Mar '15

Dear all, I am using Coot 0.7.2 and phenix 1.9-1692 on Ubuntu 13.10 and I have the following error message when I try to regularize zone, edit Chi angles or fix rotamer outliers. Error message :"Refinement setup failure. Failed to find restraints for : 'residue list' " Apparently a cif dictionary is missing that should be output by phenix to be used by coot. Does anyone has any idea? Thanks in advance. Benoit --

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on Phenix refine
by Smith Liu 19 Mar '15

19 Mar '15

Dear All, Will you please tell me which strategy of Phenix refine is for reciprocal space refinement? In the log, I often see "XYZ individual (reciprocal space)", will you please let me know whether "XYZ individual (reciprocal space)" is caused by "XYZ coordinates" or by "Optimize X-ray/sterochemistry weight"? Smith

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on the eff file
by Smith Liu 19 Mar '15

19 Mar '15

Dear All, Someone told me from the refine eff file, I can know what is my strategy for my refinement. I have run 2 refines with the same input files, For one refine, in the graphical interface I have checked xyz-coordinates, Real-space, Individual B-factors, Occupanies, Optimize X-ray/sterochemistry weight, Automaticaly orrect N/Q/H erros. For the other refine, I only checked XYZcoordinates, Real-space and Autonomously correct N/Q/H errors. I have checked the eff files from the 2 diffrent refines, but I cannot find any diffrence in the eff file. Thus will you please tell me how to find the diffrence in the 2 eff files? Or my strategies for each refine was recorded in the other files? I am looking forward to getting your reply. Smith

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the command to open the *.eff file
by Smith Lee 19 Mar '15

19 Mar '15

Dear All, Will you please tell me the command to open the *.eff file? I want to get the stratgies for my refinement. Smith

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phenix.development.optimize_model
by Colin Levy 19 Mar '15

19 Mar '15

Hi, I am running a Phenix development installation (dev_1977) and used the phenix.development.optimize_model option on a project of mine refined at 1.9Å. The output has certainly improved the R factors but I was curious as the refined model which is a rather globular structure has been refined utilising 17 TLS groups and anisotropic B factors. In its current state of development, how robust are these refinement choices and on what basis are they being determined? They differ somewhat from what I might have invoked manually? Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.levy(a)manchester.ac.uk On 12/03/2015 15:19, "phenixbb-request(a)phenix-online.org" <phenixbb-request(a)phenix-online.org> wrote: >Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > >To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb >or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > >You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of phenixbb digest..." > > >Today's Topics: > > 1. Announcement and call for abstracts: Structural > Bioinformatics microsymposium at ECM29, August 23-28, Rovinj, > Croatia (Capitani Guido (PSI)) > 2. how to correct residuess with missing atoms (Smith Liu) > 3. Re: how to correct residuess with missing atoms (Joel Tyndall) > 4. RESOLVE density modification (Mark A Saper) > 5. Re: RESOLVE density modification (Terwilliger, Thomas Charles) > 6. Nitric Oxide metal.edits not working? (Yarrow Madrona) > 7. Re: Nitric Oxide metal.edits not working? (Edward A. Berry) > 8. Group B factor refinement not working for low resolution data (??) > 9. Re: Group B factor refinement not working for low resolution > data (Pavel Afonine) > 10. Re: Group B factor refinement not working for low resolution > data (Phoebe A. Rice) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Fri, 6 Mar 2015 13:29:51 +0000 >From: "Capitani Guido (PSI)" <guido.capitani(a)psi.ch> >To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> >Subject: [phenixbb] Announcement and call for abstracts: Structural > Bioinformatics microsymposium at ECM29, August 23-28, Rovinj, Croatia >Message-ID: > <D324C9581FD3114280044EDC6357A3E51BCE66CD(a)MBX114.d.ethz.ch> >Content-Type: text/plain; charset="us-ascii" > >Dear Colleagues, > >The 29th European Crystallographic Meeting (ECM29), to be held on August >23-28 in Rovinj, Croatia, will feature a Structural Bioinformatics >microsymposium >(http://ecm29.ecanews.org/programme/microsymposia/#ms10). All structural >bioinformatics topics with relevance to macromolecular crystallography >are welcome. >Abstract submission (for oral or poster presentation) is available at >http://ecm29.ecanews.org/participate/abstract-submission/, with deadline >March 23. >The final program will encompass two 30-min talks from invited speakers, >three 20-min talks chosen from the submitted abstracts, and poster >presentations. >Looking forward to many interesting contributions; with best regards, > >Guido Capitani > > > >Dr. Guido Capitani >Paul Scherrer Institute >OFLC/110 >5232 Villigen PSI >Switzerland >guido.capitani(a)psi.ch >Tel. +41 56 310 47 22 >http://www.psi.ch/lbr/capitani_-guido >http://www.eppic-web.org > > > > > > >------------------------------ > >Message: 2 >Date: Sun, 8 Mar 2015 18:11:19 +0800 (CST) >From: "Smith Liu" <smith_liu123(a)163.com> >To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> >Subject: [phenixbb] how to correct residuess with missing atoms >Message-ID: <46870f8b.b136.14bf8de1901.Coremail.smith_liu123(a)163.com> >Content-Type: text/plain; charset="gbk" > >Dear All, > >Is any function of Phenix or some other software which can be used to >correct residuess with missing atoms in the PDB file? > >I am looking forward to getting your reply. > >Smith >

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Ramachandran results from Structure_comparison tool
by Emilia C. Arturo (Emily) 18 Mar '15

18 Mar '15

Hello, I've just run the Structure comparison tool for the first time using phenix 1.9-1692. All the results tabs--except the Ramachandran tab--have per-residue values throughout the length of the ~450-residue sequence; the Ramachandran tab has values only through residue 429. The sequence file included with the run contains 453 residues. Each of the pdb files input to the run have between 445 and 450 residues each. Throughout the length of each model, all models are 100% sequence-identical to each other and to the sequence file. Is it a known bug, that the Ramachandran values are not output for all the residues for which there are values in the other tabs? Emily Arturo Ph.D. program in Biochemistry, Drexel Univ College of Medicine Jaffe lab, Fox Chase Cancer Center Philadelphia, PA

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labelit compatibility with mosflm
by Ursula Schulze-Gahmen 18 Mar '15

18 Mar '15

I tried to use LABELIT for the first time. I am using the version that comes with Phenix-dev-1951 (automatically installed through sbgrid). The program found some promissing solutions, but ends with the error: mosflm versions after 7.1.0 not supported It also doesn't seem to know ALS beamline 8.3.1 Any suggestions how to deal with this? Thanks 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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