- phenixbb - phenix-online.org

Gordon Research Conference on Diffraction Methods
by Edward Snell 01 Jun '16

01 Jun '16

While not a Phenix posting, we do encourage attendance from the usual suspects! We'd like to remind you to register for the Gordon Research Conference on Diffraction Methods to be held at Bates College in Lewiston, Maine, July 17th-22nd 2016. The conference is themed around "Probing the structure and dynamics of macromolecules" and details of the program are at https://www.grc.org/programs.aspx?id=11655. The closing date for applications is June 19th 2016, about 5 weeks away, however GRC conferences have a limited number of participants and we will close registration early if that number is reached. Please join us in Maine this summer for the 40th anniversary of this meeting. If you are planning on attending, please note the deadline, and the growing potential that registration may close earlier. Thanks, Eddie Snell and Arwen Pearson - Chair and co-chair for 2016. Edward Snell Ph.D. CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, University at Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu Heisenberg was probably here!

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rosetta_refine connecting non-consecutive residues around break in chain
by wtempel 27 May '16

27 May '16

Hello, can one prevent rosetta_refine from connecting two residues that surround a gap? For example, how do I keep near-by residues 108 and 115 apart when 109 through 114 are missing? Thank you. Wolfram Tempel

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Fwd: Re: Scultor model with gaps included
by Gabor Bunkoczi 26 May '16

26 May '16

Apologies, this should have been directed to the mailing list. Gabor -------- Original Message -------- Subject: Re: [phenixbb] Scultor model with gaps included Date: 2016-05-25 14:33 From: Gabor Bunkoczi <gb360(a)cam.ac.uk> To: Joseph Brock <joseph.brock(a)ki.se> Dear Joseph, apologies for the late response, and sorry for the trouble. Please find some answers inlined. On 2016-05-24 15:10, Joseph Brock wrote: > Dear Phenix community, > > I was hoping if someone could help me with using Phaser correctly, > since I can't seem to produce the desired search model. > > The first thing that I was wondering about is that the CLUSTAL > alignment from the log file is quite different to the .aln alignment I > made with phenix --> other tools --> multiple sequence alignment. Why > is a sequence alignment required as input if sculptor performs it's > own internally? Sculptor can perform sequence alignment, but the algorithm is relatively basic, and you can get much better results with an external method (such as HHPRED), and hence alignment input is preferred over the target sequence. The alignment selected is printed into the logfile for reference. On the other hand, Sculptor does align the structure of your model chain to the sequence of your model (this is a surprisingly non-trivial task). However, this alignment should be close to 100% identical, unless a mistake has been made (such as using the wrong alignment file). You should get a warning if the sequence identity is too low. It is normally OK to have a couple of mismatches (such as having SeMet in the model structure with translates to "X" and not as "C"). > > My model sequence aligned to my target sequence in the log file has > several gaps in the alignment . For e.g., > > MASTER ......AASFIMV...... > CHAIN_A ......AKM--MF....... > > I would like to great a search model in which the residues aligned to > gaps in the MASTER chain are included, however the resulting sculptor > .pdb file has these residues removed. Shouldn't they be inserted so > that the rest of the chain is in the correct register? You need to do homology modelling to achieve this, as an insertion can affect the whole structure. Sculptor is designed for quick model improvement, and just renumbers/renames residues. However, the new residues numbers should reflect your sequence, i.e. in your example alignment the two methionines on both sides of the gap will get a non-consecutive number and are displayed as non-bonded in e.g. Coot. > > If anyone can let me know the parameters to allow this, I would > greatly appreciate it. I tried unselecting 'gap' in main-chain > deletion scope and some other variations, but this didn't seem to > help. > > I seem to get the same result even if I change the target index from 1 > to 2 in the associated .aln alignment. Does anyone know why this is? Hmm, this does not sound right. Can you send me the logfile so that I can have a look (please use my direct email address)? Best wishes, Gabor > > Apologies if this is quite obvious, I have been reading the > documentation but can't seem to figure it out. > > All the best, > > Joseph. > > Joseph Brock | PhD > Division of Physiological Chemistry II > Department of Medical Biochemistry and Biophysics > Karolinska Institutet > Scheeles väg 2 > SE-171 77 Stockholm, Sweden > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org -- ################################################## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##################################################

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Appropriate model_vs_data usage over part of a structure
by Andy Watkins 25 May '16

25 May '16

Perhaps necessary preface: I am largely learning as I go, and large parts of Phenix (and the details of refinement data file formats) are still black boxes for me. Suppose I have a model of one chain of a complex and an .mtz describing the entire complex. I have performed some refinement procedure altering the model of that single chain. My aim is to determine how this refinement procedure has affected the fit to the experimental data--or, really, the subset of the experimental data expected to be relevant for my model. For obvious reasons, phenix.model_vs_data chain_A.pdb whole_complex.mtz phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz are undesirable: they evaluate the model of a single chain against the whole complex's data, and there's obviously a lot of unsatisfied electron density. So, while this command *works*, it reports an unrepresentative fit. (In theory, one solution to my problem would be to re-combine each chain's refined version, then run model_vs_data on the recombined, refined complex. I'm interested nonetheless in how it would work on the chains separately. Now, during the refinement procedure, we of course generate .ccp4 density maps for the individual chain models: phenix.maps chain_A.pdb whole_complex.mtz which produces the ccp4 file as well as, crucially, chain_A_map_coeffs.mtz. Attempting to employ that resulting .mtz file, i.e. phenix.model_vs_data chain_A.pdb whole_complex.mtz phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz leads to an evocative error: Sorry_No_array_of_the_required_type: No reflection arrays available. My highest suspicion is that I need to alter maps.params in a particular way so that reflection arrays are also output to model_map_coeffs.mtz. I could also imagine that I need to be using another program entirely! Thanks in advance for whatever help you can provide; unfortunately, I can't provide any input files.

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July ACA meeting in Denver early registration still open!
by Terwilliger, Thomas Charles 24 May '16

24 May '16

?Hi Phenix colleagues! Heading to Denver for ACA's Annual Meeting in July? Early registration ends May 31 (abstracts still being accepted too!) See: http://www.amercrystalassn.org/2016-meeting-homepage ?All the best, Tom T Tom Terwilliger (2016 ACA President)

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Scultor model with gaps included
by Joseph Brock 24 May '16

24 May '16

Dear Phenix community, I was hoping if someone could help me with using Phaser correctly, since I can't seem to produce the desired search model. The first thing that I was wondering about is that the CLUSTAL alignment from the log file is quite different to the .aln alignment I made with phenix --> other tools --> multiple sequence alignment. Why is a sequence alignment required as input if sculptor performs it's own internally? My model sequence aligned to my target sequence in the log file has several gaps in the alignment . For e.g., MASTER ......AASFIMV...... CHAIN_A ......AKM--MF....... I would like to great a search model in which the residues aligned to gaps in the MASTER chain are included, however the resulting sculptor .pdb file has these residues removed. Shouldn't they be inserted so that the rest of the chain is in the correct register? If anyone can let me know the parameters to allow this, I would greatly appreciate it. I tried unselecting 'gap' in main-chain deletion scope and some other variations, but this didn't seem to help. I seem to get the same result even if I change the target index from 1 to 2 in the associated .aln alignment. Does anyone know why this is? Apologies if this is quite obvious, I have been reading the documentation but can't seem to figure it out. All the best, Joseph. Joseph Brock | PhD Division of Physiological Chemistry II Department of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 SE-171 77 Stockholm, Sweden

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Senior Research Assistant position - MD Anderson Cancer Center
by Leonard,Paul 23 May '16

23 May '16

Dear all, This post is to bring your attention to a job opportunity for a Senior Research Assistant position at the University of Texas, MD Anderson Cancer Center (in Houston, Texas, USA). MD Anderson Cancer Center is the number one cancer center in the United States and a center of excellence for both oncology treatment and research. This is an opportunity to join a dedicated team of researchers that are working together to develop new cancer therapeutics to positively impact the lives of our patients. We are looking for a highly motivated individual with experience in molecular biology and protein production to work within our structural biology team to support research projects across the MD Anderson research community and the drug discovery pipeline of the Institute for Applied Cancer Science. The research that stems from the proteins produced has a direct impact on the lives of our patients. Salaries are competitive and based on the level of experience of the applicant. We are looking for applicants with a Bachelors or Masters degree in Biochemistry, Biotechnology, Pharmacology or a related subject. Previous experience working in a research lab environment is desired. The ideal candidate will have previous molecular biology or protein purification experience. For more information and to submit a job application please refer to the job posting… https://mdanderson.referrals.selectminds.com/jobs/sr-research-asst-genomic-… We look forward to reviewing your application. Please use the above link to submit your application, CV and cover letter. Best wishes, Paul Leonard The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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ncs average map
by Jarrod Mousa 21 May '16

21 May '16

Hi all I am trying to use phenix refine to NCS average my density map during refinement. If I check refinement, I get an error saying 'Missing a map type defiinition for one or more CCP4 or XPLOR maps." If I try to upload a 2Fo-Fc map generated from FFT map coefficients, I get an error saying that phenix does not recognize the file. Any tips or other methods to calculate such a map? thanks, Jarrod Mousa

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Postdoc positions at Arizona State Uni: algorithm development for XFEL data
by Nadia Zatsepin 19 May '16

19 May '16

*Open positions: 2 Postdoc positions in XFEL Biophysics at Arizona State University.* Full details & how to apply: *https://physics.asu.edu/about/employment-opportunities <https://physics.asu.edu/about/employment-opportunities>* We are applicants for 2 postdoctoral researcher positions for the development of algorithms for biological X-ray free electron laser (XFEL) data, both in crystallography and solution scattering. The successful applicants will become part of an interdisciplinary team at ASU working on solving important biological questions using XFELs. This is a two-year Postdoctoral appointment with the possibility of extension to a maximum of three years. *Objectives* The objective of these postdoctoral researcher positions is to develop algorithms for improving data accuracy in SFX through modeling and optimization, develop novel phasing methods which exploit the full spatial coherence of the XFEL for 2D and 3D nanocrystals, and/or develop structure-determination methods that can be applied to samples that cannot be crystallized, through XFEL fast solution scattering. *Essential Functions of the position:* - Develop improved algorithms and software for analyzing biological XFEL data (static and time-resolved crystallographic or solution scattering data). - Analyze and present results at conferences, workshops, seminars and technical meetings. - Document and publish research results in peer-reviewed scientific or technical journals. - Contribute to XFEL data analysis workshops organized by the Group The successful candidates are expected to support the analysis of serial femtosecond crystallography experiments at the Linac Coherent Light Source (LCLS), SPring-8 Angstrom Compact free electron Laser (SACLA), the European X-Ray Laser (XFEL), or other applicable x-ray sources (XFELs or 3rd generation synchrotrons). This work is complementary to XFEL data analysis work in the NSF BioXFEL Science and Technology center (STC), and so the candidates will interact and collaborate with students and postdoctoral researchers working in the BioXFEL STC. They will report to the PI for the project. *Required Qualifications:* - PhD in related field such as physics, biophysics, bioinformatics, structural biology, by time of appointment. - Experience in analysis of X-ray diffraction imaging or crystallographic data. - Demonstrated algorithm and/or code development. - Demonstrated publication record in peer-reviewed literature; and experience in presenting research results to large audiences. - Demonstrated ability to perform independent research and in a diverse team environment to achieve program goals in a timely fashion. - Demonstrated fundamental verbal and written communication skills (in English) necessary to work in a multidisciplinary team environment, author technical and scientific reports and publications, and deliver scientific presentations. *Desired Qualifications:* - Experience with X-ray experiments at synchrotrons or XFELs related to high-resolution imaging or crystallography. - Experience and familiarity with coherent x-ray imaging experiments. - Experience with analyzing and solving protein structures. - Demonstrated programming experience in C and Python; experience with , web-interface development - Experience with parallel programming and large data sets. *To apply, *please submit as a single PDF document: (1) a cover letter which includes the names and email addresses of three references, (2) a curriculum vitae with a list of publications. PDF application materials should be submitted via the employment application portal. <https://physics.asu.edu/content/postdoc-position-job-11577-0> *Applications will be reviewed beginning June 15, 2016.* If not filled, every week thereafter until the search is closed. *Anticipated starting date: August 2016. * Please email nadia.zatsepin(a)asu.edu for more information. -- Nadia Zatsepin Assistant Research Professor Dept of Physics PSF246 Arizona State University +1 480 727 6444 nadia.zatsepin(a)asu.edu *http://www.public.asu.edu/~nzatsepi/ <http://www.public.asu.edu/~nzatsepi/>*

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Rfree doesn't decrease and keeps around 36%, High ramachandran outlier, High RMSD
by chen c 13 May '16

13 May '16

Dear all, I am solving a structure which diffracted to 2.8 angstrom resolution and containes 8 molecules (MW:12 kDa) per ASU. It's noteworthy that though the model used for molecular replacement shares 50% sequence identity with my protein, however, severe clashes were found as listed below: Packing Table ------------- Solutions accepted if total number of clashes <= 5% of trace atoms i.e. total number of clashes <= 32 AND if number of clashes <= 5% of trace atoms for each ensemble i.e. ensemble1: number of clashes <= 4 # # #Clash Packs SpaceGroup Annotation 1 17 NO C 2 2 21 ... PAK=11 LLG=802 RFZ=3.8 TFZ=9.3 Only after I changed the packing criteria from 5% to 100%, can I get the solution. Severe clashes and even coincidence of different molecules were found as briefly listed below: Molecule A (C-terminal) vs Molecule D (N-terminal) of neighbouring ASU Molecule B (C-terminal) vs Molecule C (N-terminal) Molecule C (C-terminal) vs Molecule D (C-terminal) Molecule E (C-terminal) vs Molecule G (N-terminal) Molecule F (C-terminal) vs Molecule H (N-terminal) Molecule G (C-terminal) vs Molecule G (C-terminal) of neighbouring ASU Molecule H (C-terminal) vs Molecule H (C-terminal) of neighbouring ASU Upon this, I manually rebuild the structure in COOT and particularly deleted those coincided atoms. Then I refined the structure in phenix. However, all the refine gives a bad result, namely, RMSD(angle) at 1.8-2.1, RMSD(bond) at 0.015-0.02, The Rwork/Rfree at around 0.28/0.36, Ramachandran outlier + Rotamer outlier at around 15-20%. I tried a lot of refinement strategy and the current status is : RMSD(angle)= 1.545, RMSD(bond) = 0.01, Rwork/Rfree = 0.290.36, Ramachandran outlier=11.3%,Rotamer outlier =1.5%. The data set belonged to C2221 and phenix.xtriage analysis reflects no twinning or pseudotranslation problem. In addition, there are two beta-turns in each molecule which displays poor electron density and geometry. And this two loop are the very residues which appears in disallowed regions in ramachandran diagram apart some other residues. However, these residues should have little effect on the R factor considering of their low contribution to the overall structure due to their poor electron density. Has anyone has experiences about this? Your help and advice is greatly appreciated! Thank you! Chen -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China Tel:+86-10-62772291 Fax:+86-10-62773145 E-mail:[email protected] 北京市海淀区清华大学生命科学馆201-212室邮编：100084

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occupancy refinement with constrained groups
by Schnicker, Nicholas J 13 May '16

13 May '16

Dear all, I am trying to do use constrained groups with occupancy refinement but struggling with syntax. I am trying to define selection1 as 2 different atoms and selection2 as another 2 different atoms. Therefore I want the 2 atoms in selection1 to have the same occupancy and the atoms in selection2 to have the same and the sum of selection 1 and 2 will be 1. If someone could help me with this syntax I would appreciate it! I have tried using brackets to separate selections but phenix doesn't recognize this. I can provide more information if needed, it's just a complicated scenario. Thanks! Nick

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FreeR flags from AutoBuild
by Sam Tang 13 May '16

13 May '16

Dear all May I enquire a simple question about AutoBuild - I input an experimental data (ccp4 mtz from Aimless) and a model from Phaser-MR to AutoBuild hoping that some mis-fit flexible regions could be re-build. May I know if the output mtz *overall_best_refine_data.mtz* contains the same FreeR flags as in the input, or would AutoBuild generate a new set of FreeR? Or in other words, are the R values directly comparable if I refine against the input experimental data mtz or the overall_best_refine_data.mtz? Thanks! Cheers Sam Tang Biochemistry Programme, School of Life Sciences, CUHK

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FW: [SA_Scat] 4th Annual CCP-SAS Project Meeting
by Kushol Gupta 13 May '16

13 May '16

---------- Forwarded message ---------- From: <stephen.king(a)stfc.ac.uk> Date: Mon, May 9, 2016 at 5:27 AM Subject: [SA_Scat] 4th Annual CCP-SAS Project Meeting To: sa_scat(a)iucr.org Dear Colleagues, We are pleased announce the 4th Annual CCP-SAS Project Meeting to be held at the NIST NCNR, Gaithersburg MD, USA from Mon 23 through Wed 25 May 2016. CCP-SAS includes the SASSIE and SCT suites of 'atomistic' modelling software. The Meeting program is available online at http://www.ccpsas.org/Meetings/Fourth/Program.html This year the Meeting also includes two 'hands-on' Tutorial Sessions on Wed 25 May: one aimed at those who wish to learn how to incorporate additional modules into the SASSIE Framework, and another aimed at those who wish to learn about wrapping applications for Web deployment using GenApp. Registration for the Meeting and Tutorials is FREE, but space is limited and places will be allocated on a first-come, first-served basis. IMPORTANT: As the meeting is being held on the NIST Campus, registration with NIST is mandatory. Please follow the 'Registration' link on the above webpage. Photo ID will be required for entry. There is also the opportunity to present relevant posters on Mon 23 May. Please contact Prof Paul Butler (pbutler(a)utk.edu<mailto:[email protected]>) if you would like to do this. On Tue 24 May there will be a special Workshop for potential future collaborators, software developers, and funders. Attendance at this Workshop is by invitation only. Please also contact Paul Butler (pbutler(a)utk.edu<mailto:[email protected]>) if you might like to contribute to these discussions. We hope you can join us! The CCP-SAS Team

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bug?
by Patrick Loll 12 May '16

12 May '16

I just ran into something that might be a small bug (phenix 1.10.1-2155) Background: I have a problem data set for which the unit cell is too small to hold we thought we were crystallizing (which probably means we crystallized the wrong protein). In any case, I ran the data through Xtriage, supplying the sequence file for the too-large protein, even though I knew this is probably not correct. This sequence file contains 264 residues. I was surprised to see that the program returned with a perfectly reasonable estimate of the Matthews coefficient, making me briefly hopeful that I had been doing the calculation incorrectly. Alas, not so; when I dig through the log file, I find the following: ____begin excerpt_______________________________________________________________ determining composition from sequence file /xxxx/seq.dat Too many residues to fit in the ASU resetting numer of residues in monomer to 26 =================== Solvent content and Matthews coefficient ================== Crystallized molecule(s) defined as 264 protein residues ------------------------------------------------------------------- | Solvent content analysis | |-----------------------------------------------------------------| | Copies | Solvent content | Matthews coeff. | P(solvent content) | |-----------------------------------------------------------------| | 1 | 0.666 | 3.68 | 0.621 | | 2 | 0.331 | 1.84 | 0.379 | ------------------------------------------------------------------- Best guess : 1 copy in the ASU _____end excerpt_______________________________________________________________ So it seems as though the program, when confronted with a protein mass that’s too large for the AU, divides the mass by 10 and tries again. However, this is not clear from the results; in the results section, it states “Crystallized molecule(s) defined as 264 protein residues." So a user might be misled into thinking that everything is OK, when in fact it’s not… Cheers, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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BCA/CCP4 Summer School 2016 - Applications now open
by Airlie McCoy 10 May '16

10 May '16

I am pleased to announce that applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond Light Source from Sunday 21st August to Friday 26th August 2016 Applications will close Friday 13th May. The registration fee of the school has been kept low due to the generous sponsorship of the BCA and CCP4. Note that up to 10 free places are available to BBSRC funded students. For a draft programme and application details see: http://www.diamond.ac.uk/Home/Events/2016/BCA-Summer-School.html The BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new to crystallography. Its dual aims are to provide comprehensive training in crystallography and to promote best practise within the British crystallographic community. The lectures cover the gamut of techniques required for a structure solution, from protein expression through to structure validation. Intensively supervised computer tutorials enable students to relate the theory presented in the lectures to practice. Although CCP5 programmes will primarily be used in these tutorials, the aim will be to approach crystallographic questions in a software-agnostic manner. There will also be a crystal manipulation and cooling workshop. (Note that the course is scheduled during Diamond synchrotron downtime, so there will not be active data collection at the Diamond beamlines.) We recognise that an active social programme plays a role in enabling students to make links that may be maintained throughout a research career. There will be a conference dinner, and a number of other events, including a boat trip on the Thames from Oxford. Airlie McCoy

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Research Technician Position at Structural Biology Lab at University of Southern California
by Xiao Lei 07 May '16

07 May '16

Dear All, The Lin Chen laboratory at the University of Southern California is seeking a research technician to join the lab. The Chen lab is interested in the structure and function of molecular complexes that control cell signaling and gene expression. We use a multi-disciplinary approach that combines structural biology, chemical biology, biochemistry/cell biology, and computational biology/bioinformatics to study the molecular basis of signal transduction and transcription regulation. For more detailed description of our research, please visit the lab page: http://structure.usc.edu/ Job Responsibilities Include: Assist postdoctoral fellows and graduate students in the lab on a variety of biochemical and biophysical studies, including gene cloning, protein expression, purification, and characterization of purified protein by various biochemical and biophysical techniques, and protein crystallization. The technician may also be involved in developing new techniques to study the structure and function of the genome. The technician is also expected to take a small amount of lab managing duty such as ordering and organizing lab supplies,. Commitment of 1 year is required; 2 years is preferred, the position is grant-funded and renewable Preferred Qualifications: • BS in Biochemistry, or Chemistry, or Molecular Biology, or related field • 2 years lab experience • Working knowledge of laboratory equipment and research protocols • Must be meticulous, detail-oriented, and responsible • Basic biochemistry, molecular biology and chemistry knowledge To apply for this position, Please send CV, three names of reference and a cover letter to: linchen(a)usc.edu Best Regards.

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autoBuild error, OSError: [Errno 12] Cannot allocate memory
by luzuok 06 May '16

06 May '16

Hello, The autobuild had been running for almost 2 hours in my Desktop, but it suddenly stopped and posed an error message as indicated below. Is this caused by my insufficient memory? Best wishes! Luzuokun Splitting work into 4 jobs and running with 2 processors using sh background=True in /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0 Starting job 1...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_4.log Starting job 2...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_5.log Starting job 3...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_6.log Starting job 4...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_7.log Traceback (most recent call last): File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 2372, in AutoBuild_build_cycle self.AutoBuild_rebuild_cycle_run() File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 4714, in AutoBuild_rebuild_cycle_run always_reuse_model=always_reuse_model) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 7589, in AutoBuild_build_refine mtz_file=mtz_file,mtz_ref_file=mtz_ref_file) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 7833, in run_standard_build_in_parallel r.run(out=sys.stdout) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/run_group_of_wizards.py", line 294, in run self.start_run(run_file,last=is_last) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/run_group_of_wizards.py", line 604, in start_run cmd+" "+self.add_double_quote(run_file,escape_space=False)) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/libtbx/easy_run.py", line 160, in __init__ close_fds=not subprocess.mswindows) File "/usr/local/phenix-1.10.1-2155/base/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/local/phenix-1.10.1-2155/base/lib/python2.7/subprocess.py", line 1223, in _execute_child self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory -- 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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Re: [phenixbb] Self Rotation Function
by Sharan Karade 04 May '16

04 May '16

Thank you for your valuable Edward, Patrick, Francis. I will try with your suggestions. And let you know the results. On 4 May 2016 20:03, "Edward A. Berry" <BerryE(a)upstate.edu> wrote: On 05/04/2016 10:17 AM, Patrick Loll wrote: > You won’t see peaks in the self-rotation function unless the AU contains > non-crystallographic rotational symmetry, which frequently is not the case > (just because you have multiple copies of your protein in the AU does not > imply that they are arranged in any specific, symmetric manner). And even > if there is rotational NCS, if the axis of rotation is parallel to a > crystal symmetry operator, the effect of the NCS will be masked. So > everything may be working as it should. > > If you’re not certain if you have the program working correctly, then I > suggest that you find a structure in the PDB that contains rotational NCS, > download the structure factors, and calculate the self-rotation map, as a > positive control. > > Try bacterioferritin (in a low-symmetry space group) or GroEL ! > On 4 May 2016, at 12:10 AM, Sharan Karade <sharankarade(a)gmail.com> wrote: >> >> Hello everyone, >> >> i am working on data set which has resolution of 2.8 A >> space group C2, the protein have 394 a a . when i estimate Mathews >> coefficient it shows four to five molecules in asymmetric unit. when i try >> to get self rotation function Map by default parameter (10A-3A and 25 >> radius of integration) i was not getting any peak at all 180, 90, 120, 60. >> Or radius of integration affect the results. >> >> Can anybody please help me to sort out with this problem, welcome for >> suggestions, thanks in advance. >> >> -- >> Sharan >> C/O Dr. J V Pratap >> Senior Research Fellow, >> CSIR-Central Drug Research Institute, >> Lucknow >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > > > > --------------------------------------------------------------------------------------- > Patrick J. Loll, Ph. D. > Professor of Biochemistry & Molecular Biology > Director, Biochemistry Graduate Program > Drexel University College of Medicine > Room 10-102 New College Building > 245 N. 15th St., Mailstop 497 > Philadelphia, PA 19102-1192 USA > > (215) 762-7706 > pat.loll(a)drexelmed.edu > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > >

1 0

Self Rotation Function
by Sharan Karade 04 May '16

04 May '16

Hello everyone, i am working on data set which has resolution of 2.8 A space group C2, the protein have 394 a a . when i estimate Mathews coefficient it shows four to five molecules in asymmetric unit. when i try to get self rotation function Map by default parameter (10A-3A and 25 radius of integration) i was not getting any peak at all 180, 90, 120, 60. Or radius of integration affect the results. Can anybody please help me to sort out with this problem, welcome for suggestions, thanks in advance. -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

4 3

Phenix.multi_crystal_average
by Sam Tang 03 May '16

03 May '16

Hello colleagues May I enquire if the captioned programme is still supported in the latest version of Phenix and, if not, which programme is now in place for this? Thanks in advance. Cheers Sam Tang Biochemistry Programme, School of Life Sciences, CUHK

2 4

CCN submissions
by Nigel Moriarty 02 May '16

02 May '16

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission in the July 2016 issue is 1 June 2016. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. 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

1 0

Refmac error using PDB coordinates generated by Phenix PDB File Editor
by Xiao Lei 29 Apr '16

29 Apr '16

Hi Phenixbb members, I'm using Phenix PDB File Editor under Phenix GUI "Model Tool" to change occupancy of two short 7 polyalanine alpha helix peptide chain (chain I and K, placed in reverse orientation of each other in one region (or density blob) of my model, each chain half occupancy) , I can change the occupancy very easily with the tool, but I have two types of errors using the coordinates generated by the tool in Refmac. 1. If I set chain ID of chain K to chain I with the same residue number with half occupancy but in reverse order (Chain I, Ala7th--13th 0.5 occupancy and Chain I, Ala7th--13th 0.5 occupancy) , Refmac could not refine the model with an error message below: I am reading library. Please wait. mon_lib.cif ERROR : ALA : duplicated atom_name : "N ". chain: II residue: 7 ERROR : ALA : duplicated atom_name : "CA ". chain: II residue: 7 ERROR : ALA : duplicated atom_name : "CB ". chain: II residue: 7 ERROR : ALA : duplicated atom_name : "C ". chain: II residue: 7 ERROR : ALA : duplicated atom_name : "O ". chain: II residue: 7 IERR = 1 There is an error. See above ===> Error: Fatal error. Cannot continue. I understand Refmac can not allow two peptide chain with the same ID and residue number if both peptides are full occupancy (1), but why in this case even half occupancy of the same chain ID and residue number is not tolerated? 2. If I set chain ID of chain K and chain I half occupancy (Chain K, Ala7th--13th 0.5 occupancy and chain I, Ala7th--13th 0.5 occupancy) , put chain K and chain I in the same density blob with reverse direction, and run Refmac, this time Refmac can finish but gave me error message in log file as below: I am reading library. Please wait. mon_lib.cif INFO: link is found (not be used) dist= 1.486 ideal_dist= 1.240 ch:II res: 7 ALA at:N .->ch:KK res: 11 ALA at:O . INFO: link is found (not be used) dist= 1.625 ideal_dist= 1.080 ch:II res: 8 ALA at:O .->ch:KK res: 9 ALA at:O . INFO: link is found (not be used) dist= 1.584 ideal_dist= 1.400 ch:II res: 10 ALA at:N .->ch:KK res: 11 ALA at:N . INFO: link is found (not be used) dist= 1.397 ideal_dist= 1.530 ch:II res: 10 ALA at:CB .->ch:KK res: 11 ALA at:CB . INFO: link is found (not be used) dist= 1.153 ideal_dist= 1.400 ch:II res: 11 ALA at:N .->ch:KK res: 10 ALA at:N . INFO: link is found (not be used) dist= 1.820 ideal_dist= 1.524 ch:II res: 11 ALA at:CA .->ch:KK res: 10 ALA at:CB . INFO: link is found (not be used) dist= 0.888 ideal_dist= 1.530 ch:II res: 11 ALA at:CB .->ch:KK res: 10 ALA at:CB . INFO: link is found (not be used) dist= 1.808 ideal_dist= 1.530 ch:II res: 12 ALA at:CB .->ch:KK res: 9 ALA at:CB . INFO: link is found (not be used) dist= 1.764 ideal_dist= 1.400 ch:II res: 13 ALA at:N .->ch:KK res: 7 ALA at:N . -------------------------------- I do not know why Refmac gave me this message, is it because the two helix chain (I and K) are placed in the same region, even though both with 0.5 occupancy of both chain, Refmac still automatically tries to connect the main chain atom between two different chains (I and K) because main chain atoms are placed too close to each other (Refmac think there is a link between them?) ? 3. In summary, should I use Phenix Refine instead of Refmac to handle the pdb coordinates generated by Phenix PDB file editor because Phenix Refine may have better compatibility? Thanks in advance.

3 5

build two helix run in opposite direction and set half occupancy or each in Coot
by Xiao Lei 29 Apr '16

29 Apr '16

Hi Phenixbb members, Is there a way in the Coot GUI that I can build two helix of the same sequence (or just short 5aa or 6aa peptide chains of the same sequence) that run in the opposite direction (180 degree opposite direction) of each other and set half occupancy of each peptide chain? I tried to use Calculate---> Model/fit/refine/----> add alternative conformation, but it seems I only have two options: "split single residue at C-alpha" or "split all of a single residue", which are applying to single residue only, not a short peptide chain. Thanks.

4 6

Re: [phenixbb] Rosetta refine compilation issue Centos 7
by ludovic Pecqueur 29 Apr '16

29 Apr '16

Dear Phenix developers, This is a feedback from a previous post started a long time ago when I was trying to install the rosetta interface for phenix in Centos 7. As a reminder, I could compile Rosetta with './scons.py -j8' without problem but rosetta.build_phenix_interface exited with an error message related to python. I had given up for some time but I tried again today with more luck. setting up PYTHONHOME as previously suggested was breaking something: which python /usr/bin/python python -c "import site" returns no error > export PYTHONHOME=/usr/bin/python (so the distribution's python) python -c "import site" returns "no module named site" unset PYTHONHOME python -c "import site" returns no error message. adding the path to my local PYTHON with export PATH=/where my local Python 2.7 is/bin/:$PATH was the correct fix and I could finally run rosetta.build_phenix_interface without errors. Cheers Ludovic. On Sep 28, 2015, at 3:24 AM, phenixbb-request(a)phenix-online.org wrote: > Message: 8 > Date: Thu, 24 Sep 2015 16:43:40 +0200 > From: ludovic Pecqueur <ludovic.pecqueur(a)college-de-france.fr> > To: Paul Adams <pdadams(a)lbl.gov> > Cc: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Rosetta refine compilation issue Centos 7 > Message-ID: > <0CB7F2F9-4E89-4598-92FA-58AE2526FF8D(a)college-de-france.fr> > Content-Type: text/plain; charset=us-ascii > > Hi Paul, Nigel, > > Thank you for the suggestion. > > I tried to set PYTHONHOME with > export PYTHONHOME=/usr/bin/python > or > export PYTHONHOME=to PHENIX's python > or > export PYTHONHOME=to a local python compiled from source that I use to compile programs like Pymol > > to no avail, I get the same error message. > > As I can compile Rosetta without phenix using : ./scons.py -j6 mode=release bin, do you think the problem could reside in the way rosetta.build_phenix_interface works? > > Cheers, > > Ludovic. > > > On Sep 23, 2015, at 11:09 PM, Paul Adams <pdadams(a)lbl.gov> wrote: > >> Hi Ludovic, >> >> the problems seem to occur when scons is called to compile Rosetta. I notice that the scons.py file uses the python that appears first in your path (#! /usr/bin/env python). Is it possible that this is a python that is broken in some way? >> >> Cheers, >> Paul >> >>> On Sep 23, 2015, at 9:11 AM, ludovic Pecqueur <ludovic.pecqueur(a)college-de-france.fr> wrote: >>> >>> Dear Developers, >>> >>> I have a fresh Centos 7 system and after installing Phenix I wanted to compile the Rosetta.refine module. (Rosetta from source version 2015.31.58019) >>> >>> I have succesfully compiled Rosetta but when I try to build the dedicated Rosetta for Rosetta_refine with rosetta.build_phenix_interface after setting up PHENIX_ROSETTA_PATH and ROSETTA3_DB I get the following error message: >>> >>> [XXX@...]$ rosetta.build_phenix_interface nproc=6 >>> False >>> scons: Reading SConscript files ... >>> Running versioning script ... Done. (0.1 seconds) >>> Could not find platform independent libraries <prefix> >>> Could not find platform dependent libraries <exec_prefix> >>> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] >>> ImportError: No module named site >>> CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: >>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 172: >>> main() >>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 163: >>> SConscript("SConscript", "build") >>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: >>> return method(*args, **kw) >>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: >>> return _SConscript(self.fs, *files, **subst_kw) >>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: >>> exec _file_ in call_stack[-1].globals >>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConscript", line 28: >>> subprocess.check_call(["./update_options.sh"]) >>> File "/usr/local/PROGRAMS/XTAL/PHENIX/phenix-1.10-2155/base/lib/python2.7/subprocess.py", line 540: >>> raise CalledProcessError(retcode, cmd). >>> >>> If you have any idea of what could cause the problem, I would welcome any suggestions. >>> I updated Phenix and I could compile phenix.rosetta_refine without problems on Centos 6.7. >>> >>> Thank you very much for your time and help. >>> >>> Kind regards, >>> >>> Ludovic. >>> >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> Unsubscribe: phenixbb-leave(a)phenix-online.org >> >> -- >> Paul Adams >> Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab >> Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab >> Adjunct Professor, Department of Bioengineering, U.C. Berkeley >> Vice President for Technology, the Joint BioEnergy Institute >> Laboratory Research Manager, ENIGMA Science Focus Area >> >> Building 33, Room 347 >> Building 80, Room 247 >> Building 978, Room 4126 >> Tel: 1-510-486-4225, Fax: 1-510-486-5909 >> http://cci.lbl.gov/paul >> >> Lawrence Berkeley Laboratory >> 1 Cyclotron Road >> BLDG 33R0345 >> Berkeley, CA 94720, USA. >> >> Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] >> -- >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > > > > ------------------------------ > > Message: 9 > Date: Mon, 28 Sep 2015 01:21:21 +0000 (UTC) > From: Smith Lee <smith_lee123(a)yahoo.com> > To: PHENIX User Mailing List <phenixbb(a)phenix-online.org> > Subject: [phenixbb] on Phenix10 > Message-ID: > <615863586.1820571.1443403281522.JavaMail.yahoo(a)mail.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > With the EM cryo data, I have compared the function of phenix.real_space_refine of Phenix10 and Phenix1.9-1692. For the Ramachandran favored, the new version is about 90%, the old version is about 92%. For the clashscore by Molprobity, the new version is about 30, the old version is about 20. Molprobity indicated the clashing atoms were systematically existing in the whole molecule, rather than on specific parts of the protein which may be indication of bad modelling. > Clearly the clashscore of 30 is unacceptable. Will you please give some advise on how to improve the function of new version of Phenix, considering adding H was not suitable as for the resolution was poorer than 4.0 A? > Smith >

1 0

Algorithm developer postdoc opening at Berkeley National Lab
by Nicholas Sauter 28 Apr '16

28 Apr '16

Berkeley Lab's Molecular Biophysics and Integrated Bioimaging Division <http://biosciences.lbl.gov/divisions/mbib/> is looking for a Computational Biologist Postdoctoral Fellow to work in the Sauter group. We are seeking an algorithm developer for the increasingly complex analysis of large diffraction datasets in structural biology. Current projects utilize XFEL crystallography and spectroscopy to investigate the photosynthetic mechanism of water splitting and to probe other metalloenzyme reactions. We also wish to test whether diffuse scattering can reveal correlated atomic motions in crystals. Many problems remain to be solved, including the details of how to optimally merge datasets from thousands of crystals. Our software development projects (including packages such as DIALS <http://dials.lbl.gov> and cctbx.xfel <http://cci.lbl.gov/xfel>) have been highlighted in several high-impact publications listed HERE <http://biosciences.lbl.gov/profiles/nicholas-sauter>. Candidates should have expertise in one or more computational techniques including, but not limited to, ray tracing to test underlying physical models of the diffraction, Bayesian approaches for refining model parameters, macromolecular modeling and refinement, neural networks for interpreting image features, as well as signal processing and denoising methods. Extensive data analysis experience in crystallography or from more general bioimaging backgrounds are welcome. We particularly encourage strong mathematical intuition and a track record of bringing new ideas and tools to fruition, as evidenced through written publication and clear presentation. Candidates should send an expression of interest, CV, and list of three references to *Nick Sauter, nksauter(a)lbl.gov <nksauter(a)lbl.gov>.* Further details are posted at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=82354. Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720

1 0

Weird large continuous positive density blob
by Alex Lee 26 Apr '16

26 Apr '16

Dear Phenixbb members, I have a protein (90aa length) structure with 2.3A resolution and space group P21 refined to Rfree/R to around 0.27 / 0.20. There are 3 protein dimers in one asym unit. For two dimers (chain A, B, C, D), I can see clearly continuous electron density from residue 10 to residue 89. However for the third dimer (chain E and F), I can only see clearly continuous density between residue 10 to residue 72 and lost tracing of the main chain. I did see a large electron density blob close to the third dimer. ( https://goo.gl/photos/R1SaHPKS6VLfcesb7 ; Green is positive density at 3 sigma and blue is FWT PHWT at 2sigma and 1sigma ). I do not know how to explain this blob. It seems to me that this blob is unlikely protein fragments (some parts of the blob is so chunky). Even if it's true that it's certain protein fragment between residue 73 to residue 89 of chain E or chain F, then the position of this fragment is totally different from the position of its fragment counterparts in chain A,B, C,D. I assume NCS copies (in this case maybe 3 copies) should have the same morphology as to each other. It also seems to me that this density is not from my crystal growth or harvest conditions, which has: Bis-Tris; PEG3350; PEG400 and NaCl. I do not know if Phenix Autobuild could build this automatically for me, but I'll try this later. Thanks in advance for any input on this. The density link is: https://goo.gl/photos/R1SaHPKS6VLfcesb7

2 2

(no subject)
by Alexander Grishaev 26 Apr '16

26 Apr '16

agrishaev(a)ibbr.umd.edu

1 0

Re: [phenixbb] Coot does not start up with OS 10.11 El Capitan
by Benoît Masquida 26 Apr '16

26 Apr '16

Following the suggestion from Engin, I indicate which installer I used to install coot, Coot-0.8.3-pre-5936_64bit_10.11.3.pkg found on Bill Scott’s website. Installation creates the following executable in the /bin directory: -rwxr-xr-x 1 root wheel 535 24 mar 17:32 coot Chown does not change solve the problem that the graphics do not appear. Any help still welcome. Best, Benoit Benoît Masquida b.masquida(a)unistra.fr UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB - Plateforme de Biologie 4 Allée Konrad Roentgen 67081 STRASBOURG Cedex > Le 22 avr. 2016 à 17:40, Engin Özkan <eozkan(a)uchicago.edu> a écrit : > > As far as I know, there are no issues with Coot/Phenix on El Capitan. You may need to give more info on how you actually installed Coot (and which Coot you are invoking from Phenix, which you may have set in Coot path under Preferences->Graphics in Phenix). > Engin > > On 4/22/16 4:24 AM, Benoît Masquida wrote: >> Dear All, >> >> I re-installed Quartz as suggested. Then I have more verbose messages upon launching coot from the shell (See below). I don’t know if it is a general problem or a problem related to the configuration of my machine. >> >> Thanks. >> >> Benoit >> >> mmdcd-img2:bin B.Masquida$ ./coot >> INFO:: Reading coordinate file: /Library/Coot/share/coot/standard-residues.pdb >> PDB file /Library/Coot/share/coot/standard-residues.pdb has been read. >> Spacegroup: P 1 >> initalize graphics molecules...done. >> filter_fileselection_filenames_state () >> get_active_map_drag_flag () >> use_graphics_interface_state () >> INFO:: coot.py imported >> INFO:: coot_python initialized >> Running python script /Library/Coot/lib/python2.7/site-packages/coot/coot_load_modules.py >> Good Morning B.masquida, Welcome to Coot. 0.8.3-pre >> set_display_intro_string ("Good Morning B.masquida, Welcome to Coot. 0.8.3-pre") >> Coot Python Scripting GUI code found and loaded. >> Coot Python Scripting GUI code found and loaded. >> use_graphics_interface_state () >> filter_fileselection_filenames_state () >> get_active_map_drag_flag () >> coot-bin: Fatal IO error 35 (Resource temporarily unavailable) on X server /private/tmp/com.apple.launchd.cTrzTueRvK/org.macosforge.xquartz:0. >> coot-bin: Fatal IO error 35 (Resource temporarily unavailable) on X server /private/tmp/com.apple.launchd.cTrzTueRvK/org.macosforge.xquartz:0. >> mmdcd-img2:bin B.Masquida$ >> >> >> >> >> >> Benoît Masquida >> b.masquida(a)unistra.fr <mailto:[email protected]> >> UMR 7156 GMGM >> tel: +33 3 68 85 14 81 >> fax: +33 3 68 85 13 65 >> IPCB - Plateforme de Biologie >> 4 Allée Konrad Roentgen >> 67081 STRASBOURG Cedex >> >>> Le 21 avr. 2016 à 17:10, Xiao Lei < <mailto:[email protected]>xiaoleiusc(a)gmail.com <mailto:[email protected]>> a écrit : >>> >>> Hi BM, >>> >>> If it happens after you upgrade the system, you may try re-install the Xquartz. >>> >>> On Apr 21, 2016 6:48 AM, "Benoît Masquida" <b.masquida(a)unistra.fr <mailto:[email protected]>> wrote: >>> Dear Phenix, >>> >>> The graphic window of coot does not open either launch from the shell or from Phenix GUI. Has anyone experienced (and solved) this problem on El Capitan (from Apple)? >>> >>> Thanks for your help. >>> >>> BM >>> >>> -- >>> Benoît Masquida >>> b.masquida(a)unistra.fr <mailto:[email protected]> >>> UMR 7156 GMGM >>> tel: +33 3 68 85 14 81 <tel:%2B33%203%2068%2085%2014%2081> >>> fax: +33 3 68 85 13 65 <tel:%2B33%203%2068%2085%2013%2065> >>> IPCB - Plateforme de Biologie >>> 4 Allée Konrad Roentgen >>> 67081 STRASBOURG Cedex >>> >>> _______________________________________________ >>> 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]> >> >> >> _______________________________________________ >> 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]>

2 1

Gordon Research Seminar this July
by Bradley Hintze 26 Apr '16

26 Apr '16

Attention Young scientist in crystallography and diffraction. Are you a young scientist interested in the methods in crystallography? Do you want to deepen your understanding of instrumentation, different diffraction methods, data processing, phasing, structure solution, etc.? The Gordon Research Seminar and Conference for Diffraction Methods happens July 16 - 22 (for both) at Bates College in Maine. It is a unique opportunity to interact with the researchers actively developing the exciting many methods related to crystallography and beyond. The conference is relatively small allowing close association with all in attendance allowing participants to discuss methods with those in the know. The Gordon Research Seminar is a two-day event before the Conference for those early in their career, e.g. students, postdocs, and beginning industry folks. This space allows young scientist to interact, ask questions, and discuss their science with peers. If you are interested in deepening your understanding of the methods behind crystallography, please consider applying to both the Gordon Research Seminar and Conference on Diffraction Methods. For all the details, please see: <goog_1374816820> https://www.grc.org/programs.aspx?id=16486 Apply soon! Any questions? Simply reply to this email. Thanks GRC chairs, Rike Müller-Werkmeister and Bradley Hintze

1 0

Coot does not start up with OS 10.11 El Capitan
by Benoît Masquida 22 Apr '16

22 Apr '16

Dear Phenix, The graphic window of coot does not open either launch from the shell or from Phenix GUI. Has anyone experienced (and solved) this problem on El Capitan (from Apple)? Thanks for your help. BM -- Benoît Masquida b.masquida(a)unistra.fr UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB - Plateforme de Biologie 4 Allée Konrad Roentgen 67081 STRASBOURG Cedex

2 2

phenix.polder - tool for calculating omit maps by excluding bulk solvent
by Dorothee Liebschner 21 Apr '16

21 Apr '16

Dear phenix users, Starting from the nightly build dev-2356, a new tool for calculating ligand omit-maps, called 'polder', is included in phenix. Usage: phenix.polder model.pdb data.mtz selection='chain A and resseq 123’ Phenix.polder calculates omit maps for atom selections by preventing the bulk solvent mask to flood into the atom selection area and its vicinity. The tool can be useful in cases where the density of the selected atoms is weak and possibly obscured by bulk solvent. Polder produces less biased maps compared to procedures where the atom selection occupancy is set to zero, and the atoms are included in the solvent mask calculation (in that case, the resulting difference density can have similar shape than the selected atoms). Phenix.polder excludes a larger volume from the bulk solvent and therefore prevents misinterpreting bulk solvent density as omit density. If you want to know more about how the tool is working and to see some examples, have a look at the presentation file: https://www.phenix-online.org/presentations/phenix_polder.pdf. The documentation page can be found here: www.phenix-online.org/version_docs/dev-2356/reference/polder.html Best wishes, Dorothee

4 8

fit_loops using loop_lib
by Greg Bowman 21 Apr '16

21 Apr '16

Hi all - I’m having a problem getting phenix.fit_loops to run using the loop library (loop_lib=True). The phenix.fit_loops seems to work fine without this keyword (I get a good solution for a test case), but I have 3A density and wanted to restrict solutions to the loop library for the poorer density regions. I am running this from the command line, with this input: phenix.fit_loops pdb_in=refine_35-delloop1170to1172.pdb mtz_in=refine_35.mtz \ seq_file=KRJmonomer.seq start=1170 end=1172 chain_id=B \ loop_lib=True >> fit_loops-1170to1172-looplibrary.log I am using OSX ElCapitan (10.11.3) and get this error: File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 962, in <module> fit_loops=fit_loops(args=sys.argv[1:]) File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 598, in __init__ target_time=target_time, File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 760, in run_fit target_time=target_time, File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/autosol/UserMethods.py", line 3671, in Build_fit_gaps starting_residue_number=starting_residue_number) File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/loop_lib/clustering.py", line 2063, in apply_clusters d=get_density_map(map_coeffs_array=map_coeffs_array) File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/utilities/get_density_map.py", line 54, in __init__ assert not map_coeffs_array.anomalous_flag() AssertionError The last lines of the log file are: Fitting loop with loop-library... loop_lib length (including 3 on each end): 9 DATABASE: /Applications/phenix-1.10.1-2155/modules/chem_data/loop_library/loops_9_2.5/loop_lib CLUSTER_FILE: split_clusters.pkl.gz Thanks, Greg

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clash_guard failure
by Bock, Tobias 20 Apr '16

20 Apr '16

Dear colleagues, I am trying to refine a protein-DNA complex. In this structure, 2 DNA double strands are present with 50% occupancy (or similar occupancy’s) and overlap at certain positions. Phenix.refine crashed due to a nonbonded interaction distance issue. To fix that, I tried to exclude the DNA strands using: pdb_interpretation { custom_nonbonded_symmetry_exclusions="chain E" custom_nonbonded_symmetry_exclusions="chain F" } Nevertheless, phenix.refine crashed with the same error message. Changing the “nonbonded_distance_threshold” works, but results in terrible statistics (since this applies for the complete structure, I guess). Is there a way to exclude only the DNA strands (in regard to the clash guard) or a similar approach to refine the structure? Thank you in advance for your help, Tobias ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" 50 Jahre Spitzenforschung - 50 Jahre HZI: www.helmholtz-hzi.de/50 Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Re: [phenixbb] Merging Already-Scaled MTZs
by Tim Gruene 20 Apr '16

20 Apr '16

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Jacob, I overlooked the s at mtz, i.e. I thought you wanted to re-merge a single data set. My apologize for this. Your question is correctly formulated and perfectly valid. I would try pointless (easy) or cad (a little tedious but more prone to work) followed with aimless and its keyword 'onlymerge'. Best regards, Tim On Wednesday, April 20, 2016 07:36:07 PM you wrote: > Depends on your definition of "merge." What verb would you use for the > process I am describing? > > JPK > > -----Original Message----- > From: Tim Gruene [mailto:[email protected]] > Sent: Wednesday, April 20, 2016 3:05 PM > To: phenixbb(a)phenix-online.org > Cc: Keller, Jacob > Subject: Re: [phenixbb] Merging Already-Scaled MTZs > > Dear Jacob, > > it is technically not possible to merge relfection data twice, unless you > change to a higher symmetry space group: merging means replacing symmetry > related reflections with their mean. > > For scaling this is different - couldn't you repeat the scaling step? I am > not sure if phenix contains data processing software, I thought it starts > at data analysis and structure solution. > > Cheers, > Tim > > On Wednesday, April 20, 2016 06:59:04 PM Keller, Jacob wrote: > > Dear Crystallographers, > > > > I guess it is bad practice to merge/scale already-merged/scaled mtz's, > > but I have a special reason for wanting to do so. Does anyone know how > > this can be done in Phenix? > > > > The reason is, if you're interested, that I want to detwin several > > different datasets to varying degrees, then merge them. > > > > 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 > > -- > -- > Paul Scherrer Institut > Tim Gruene > - persoenlich - > OFLC/102 > CH-5232 Villigen PSI > phone: +41 (0)56 310 5297 > > GPG Key ID = A46BEE1A - -- - -- Paul Scherrer Institut Tim Gruene - - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iD8DBQFXF9yHUxlJ7aRr7hoRArioAKDxnnJxNGZaAbV8PDmUprCJuvk7mwCg21jr wG0I05gbSvcFjrfzndkNRWY= =BHXV -----END PGP SIGNATURE-----

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Merging Already-Scaled MTZs
by Keller, Jacob 20 Apr '16

20 Apr '16

Dear Crystallographers, I guess it is bad practice to merge/scale already-merged/scaled mtz's, but I have a special reason for wanting to do so. Does anyone know how this can be done in Phenix? The reason is, if you're interested, that I want to detwin several different datasets to varying degrees, then merge them. 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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Autobuild
by Sam Tang 20 Apr '16

20 Apr '16

Dear colleagues I have recently downloaded a Windows GUI version of Phenix 1.10.1-2155. When I used AutoBuild these few days it keeps turning out the following errors: Job 1 failed: child process stderr output: command: ['phenix.autobuild', 'C:\\Users\\pcshaw\\Desktop\\NPAproc\\B13_proc\\AutoBuild_run_4_\\TEMP0\\PARAMS_1.eff', 'write_run_directory_to_file="C:\\Users\\pcshaw\\Desktop\\NPAproc\\B13_proc\\AutoBuild_run_4_\\TEMP0\\INFO_FILE_1"'] Traceback (most recent call last): File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\build\..\modules\phenix\phenix/command_line\autobuild.py", line 228, in <module> run_autobuild=run_autobuild(args=sys.argv[1:]) File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\wizard_command_line.py", line 564, in __init__ self.RunWizard() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\wizard_command_line.py", line 1001, in RunWizard self.runWizard.run() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 836, in Run self.DoNextMethod() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1004, in DoNextMethod raise AssertionError, line AssertionError: Traceback (most recent call last): File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\wizards\AutoBuild.py", line 2372, in AutoBuild_build_cycle self.AutoBuild_rebuild_cycle_run() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\wizards\AutoBuild.py", line 4626, in AutoBuild_rebuild_cycle_run refine_2fofc=refine_2fofc) File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\wizards\AutoBuild.py", line 5500, in AutoBuild_resolve_with_model hklout=hklout,labin=labin) UnboundLocalError: local variable 'labin' referenced before assignment Could I please enquire if these are due to mis-setting of parameters or in fact problems related to my recent installation? Yet another question on my mind is, is AutoMR still supported in this Windows version? I can now no longer find it in the GUI while it used to be there in the 1.7 Mac version. Kind regards Sam Biochemistry Programme, School of Life Sciences, CUHK

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phenix output graphs
by Christian Roth 19 Apr '16

19 Apr '16

Hi Phenix-Team, there are some nice graphs produced for example after refinement. If I want to save such a graph (B-Factor histogram) as jpg or so, is that possible or do I have to save the values and redraw it outside phenix? The only plot I oculd save was the B-Fac plot per residue, which wouldn't be helpful in that case. Thanks for some insight. Cheers Christian

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questions/problems with tls_as_xyz routines
by David A Case 18 Apr '16

18 Apr '16

I'm trying to use tls_as_xyz, but having some problems. 1. In the paper describing this, Urzhumtsev et al, Acta Cryst D71:1668, 2015, there seems to be something wrong with Section 6.2, which describes results on PDB entry "1dqv", syanptotagmin III. The description says that there are two copies of the molecule in the asymmetric unit, and the resolution is 2.5 Ang. However, the file with this code in the RCSB (which is indeed syanptotagmin III) has one molecule per asymmetric unit, a single chain of 296 amino acids, rather than two chains of 97 amino acids, as in Tables 2 and 3 of the paper cited above; the resolution is 3.2 Ang. And it doesn't look anything like the picture of "1dqv" in Fig. 3a. So something looks wrong; does anyone know what system Section 6.2 is using? 2. I'm asking the above because I'm having trouble with my own applications, and was hoping to check that I could reproduce the results in the paper. Apropos of that, is there a test case or example for tls_as_xyz in the phenix distribution? [I'm not all that familiar with phenix, so apologies if I've missed the easy way to find this.] 3. Here is a summary of what is not working for me. (I don't expect anyone to debug this on such little information, but thought that someone on the list might have done some similar calculation.) a. I took a small domain (residues 6-61 from GB3, PDB code 2IGD), and used Ethan Merrit's lsq_tls_fit to obtain a set of TLS tensors that best fit the deposited ADP's. The statisitcs are pretty good, indicating (not surprisingly) that motions in this domain are well characterized as a rigid body--which is why I chose this system. I just used the CA atoms for this initial study. b. I used phenix.tls_as_xyz to compute an ensemble from the TLS matrices obtained in step a. c. I then computed ADP's from the ensemble, using tools from cpptraj in Amber, (or our own codes, which give the same results). But the extracted isotropic B factors (and the anisotropic components) are much larger than the input ones. So, the ensemble is giving me what I expected: a sampling of structures whose fluctuations arise from the input TLS matrices. I've done a fair amount of due diligence in trying to track down errors on my end, but I could be making a mistake on any one of the steps above. Or, I could be mis-interpreting what I should expect to get from the tls_as_xyz procedure. I'd be happy to share details off-line with any one who might volunteer to help. ...thanks...dave case

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Application deadline is this week: CCP4/APS crystallographic school, June 21 - 29, 2016
by Sanishvili, Ruslan 18 Apr '16

18 Apr '16

Dear Colleagues, Deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered. If you have a crystallographic problem you cannot resolve independently, this school is for you. From our past experience, the majority of participants bring with them the crystallographic problems and almost all these problems are resolved at the school. Some of the publications, acknowledging the contribution of the school, are listed at http://www.ccp4.ac.uk/schools/APS-school/publications.php This school will cover popular packages such as CCP4, PHENIX, SHELX and much, much more: http://www.ccp4.ac.uk/schools/APS-2016/program.php Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts. Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue. These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found at: http://www.ccp4.ac.uk/schools/APS-2016/index.php We are looking forward to meeting you in Argonne this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Wednesday, March 23, 2016 10:26 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] Reminder, CCP4 crystallographic summer school at the APS, June 21 - 29, 2016 Dear Colleagues, This is a reminder that the application deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered. The school will take place from June 21 through June 29, 2016 at the Advanced Photon Source, Argonne National Laboratory, near Chicago. All aspects of macromolecular crystallography from data collection to structure refinement and validation, as well as functional assessment, will be covered. Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts. >From our past experience, the majority of participants bring with them the crystallographic problems they cannot resolve independently and almost all these problems are resolved at the school. Some of the publications, acknowledging the contribution of the school, are listed here: http://www.ccp4.ac.uk/schools/APS-school/publications.php Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue. These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found here: http://www.ccp4.ac.uk/schools/APS-2016/index.php We are looking forward to meeting you in Argonne this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Tuesday, February 23, 2016 7:48 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] CCP4 crystallographic summer school at the APS, June 21 - 29, 2016 Dear Colleagues, We are pleased to announce the 9th annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Title: CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 21 through 29, 2016 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 21. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Registration fees: The registration fee for the selected participants is $400 for the academic and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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Re: [phenixbb] Data processing: exhaustive search?
by Kay Diederichs 17 Apr '16

17 Apr '16

Hi Kaushik, there is no need for, and no sense in, an exhaustive search of data processing parameter space, because its dimensionality is way too high to achieve anything useful. The programs MOSFLM and XDS have undergone decades of development, and their processing defaults are carefully chosen. It is rather the user of the programs who is in charge to correctly interpret the output (which requires reading of their documentation, and some experience), and to make meaningful adjustments to (usually very) few parameters. Speaking for XDS, I recommend to read XDSwiki articles (there are tutorials and example data sets, and lots of explanations) and a book chapter that I recently wrote (#131 at http://cms.uni-konstanz.de/strucbio/diederichs-group/publications ). If you use the generate_XDS.INP script from XDSwiki, and follow the paper and the "Optimization" article, you will get good data from XDS. (There are other scripts, like autoPROC, xia2, xdsme and so on, which usually also give good results but I don't know them well.) In particular, in case of XDS there is usually no need to fiddle around with "box size, spot separation, tolerance and other parameters". The fact that you seem to try and optimize Rmerge suggests to me that you are trading precision for accuracy. Too many people still do this, but it is a legacy of the past. "Trying a combination of better frames over poorer frames" is most likely _not_ going to improve your merged intensities - this is another unfortunate and very common misunderstanding (see references 113 and 130). I hope this helps you to get better data. Kay On 16.04.2016 21:18, phenixbb-request(a)phenix-online.org wrote: > Message: 6 > Date: Sun, 17 Apr 2016 00:48:31 +0530 > From: Kaushik Hatti <hskaushik(a)gmail.com> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Data processing: exhaustive search? > Message-ID: > <CAGMFGb=B9s-j4yXmRx8_M7NPndf86puviiY9QMg=EAqaWr9thw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I have a data set diffracted to 2.7A collected at 1.54 wavelength. The data > is not of great quality with very close spots, ellipsoid spots in certain > regions of the frames and spot overlaps. Also certain frames are poorer > than rest. The crystal could not be reproduced. > > The best R merge (overall) I have achieved so far is 17% with 85% > completeness and 3 I/SigI processed in P4 space group. I feel it's possible > to process it better by identifying right values for box size, spot > separation, tolerance and other parameters. I am also suspecting a higher > symmetry space group. I believe, trying a combination of better frames > over poorer ones with improve merging statistics. > > I have so far tried processing in iMosflm and XDS. Is there a tool which > could search exhaustively trying different values for parameters and > suggest the combination which provide best merging statistics? > > Sorry if this question is not relevant in this group. > Any pointers/suggestions would be gratefully helpful. > > Thanks in advance, > Regards, > Kaushik > Molecular Biophysics Unit, > Indian Institute of Science, > Bangalore, India. -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz

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Data processing: exhaustive search?
by Kaushik Hatti 16 Apr '16

16 Apr '16

Hello, I have a data set diffracted to 2.7A collected at 1.54 wavelength. The data is not of great quality with very close spots, ellipsoid spots in certain regions of the frames and spot overlaps. Also certain frames are poorer than rest. The crystal could not be reproduced. The best R merge (overall) I have achieved so far is 17% with 85% completeness and 3 I/SigI processed in P4 space group. I feel it's possible to process it better by identifying right values for box size, spot separation, tolerance and other parameters. I am also suspecting a higher symmetry space group. I believe, trying a combination of better frames over poorer ones with improve merging statistics. I have so far tried processing in iMosflm and XDS. Is there a tool which could search exhaustively trying different values for parameters and suggest the combination which provide best merging statistics? Sorry if this question is not relevant in this group. Any pointers/suggestions would be gratefully helpful. Thanks in advance, Regards, Kaushik Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

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Re: [phenixbb] Hardward phenix.refine
by Kay Diederichs 12 Apr '16

12 Apr '16

Colin, check out the first option in the FAQ at https://www.phenix-online.org/documentation/faqs/refine.html A core i7 and a Xeon of the same generation are equally fast if their frequency is the same. The main differences are that - Xeon E3 supports ECC memory (most core i* don't) - Xeon E5 supports Dual-CPU (core i* is just one) - Xeon E7 supports multi-CPU and is very expensive - most Xeons don't have built-in graphics whereas most core i* do There are many other small differences but most of them irrelevant; inspect the Wikipedia pages! Xeons won't be faster with phenix.refine; a core i7 already has enough cores - to increase their usage you'll have to recompile as per the FAQ. HTH, Kay > > Message: 1 > Date: Mon, 11 Apr 2016 07:56:39 +0000 > From: Colin Levy <C.Levy(a)manchester.ac.uk> > To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Hardward phenix.refine > Message-ID: <773C4580-FA01-4246-86E9-2D73AFD98421(a)manchester.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > Having read the FAQ regarding hardware I have a few ideas but would greatly appreciate any input from the community or developers. > > Would anyone like to suggest the best configuration of hardware for running phenix.refine? I mainly operate in OSX but have no issue with switching operating system if I can get a faster setup. My current thoughts are either something running a 4GHz Quad core i7 or an alternative would be a 3.7GHz Quad-Core Intel Xeon E5 (iMac v Mac Pro) or equivalent Linux builds. > > I know that the i7 is reasonably fast as I have this setup in a different machine and phenix.refine runs reasonably quickly but as ever I would like it to be faster. Budget is not unlimited by any means but I would be interested in learning what an optimal setup might look like. > > 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<mailto:[email protected]> > > Manchester Institute of Biotechnology | University of Manchester | 3.020 Garside Building | 131 Princess Street | Manchester | M1 7DN

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Re: [phenixbb] Phenix Xtriage label error
by Alex Lee 12 Apr '16

12 Apr '16

Hi Dorothee and Billy, Thank you for your information! I have both I, SIGI and IPR, SIGIPR labels in my unmerged MTZ (I checked this with ViewHKL). But it seems the Xtriage only offers choices to merged mtz. I tried to choose I,SIGI, Merged option (even though my mtz is unmerged), the Xtriage output shows "anomalous flag false" and I did not get any additional anomalous information from the report. On Tue, Apr 12, 2016 at 12:16 PM, Dorothee Liebschner <dcliebschner(a)lbl.gov> wrote: > Hi Alex, > > What data labels are in the file pointless_xxx.mtz? > You can check with > > phenix.mtz.dump pointless_xxx.mtz > The output should list the available labels. > (you should see the labels also in hklview) > > You cannot leave the data labels choice blank in xtriage, as you have two > data choices in your file, so you need to tell the program which ones to > use. > > Apart from xtriage, it is always helpful to check the anomalous signal > reported in various log files from your data processing steps, such as > aimless.log and also from mosflm (I am not familiar to mosflm but I guess > it outputs also some info about anomalous signal?). > > Best wishes, > > Dorothee > > > > > > On Tue, Apr 12, 2016 at 11:08 AM, Alex Lee <alexlee198609(a)gmail.com> > wrote: > >> Dear Phenixbb members, >> >> I have a data-set of a 8 kDa protein crystal around 2.5A resolution. The >> protein crystal was soaked in potassium iodine before collecting data using >> in-house beam (1.54A wavelength). As I expected some anomalous signal from >> the iodine ion from the crystal, after I use Imosflm to index, integrate >> and scale the data (space group P3). I got four output .mtz files: >> pointless_XXX.mtz; aimless_xxx.mtz; ctruncate_xxx.mtz; >> ctruncate_xxx-unique.mtz. After I check with viewHKL, I found the only >> unmerged mtz data is pointless_XXX.mtz, the other three mtz files are >> merged. >> >> The next step I tried to use Phenix Xtriage (Linux version 1.10.1) to >> check my mtz data for anomalous completeness, I thought in this step my mtz >> should be unmerged type to see the anomalous signal, so I chose >> "pointless_xxx.mtz" as Xtriage input, but for the data labels in the >> Xtriage GUI panel, I can only have two choices of "I, SIGI, Merged" and >> "IPR, SIGIPR, Merged", it seems I do not have a choice of an unmerged mtz >> label. I decide to leave this choice blank by choosing data labels"---". >> After I click "run", Xtriage gave an error "please select labels for input >> data". >> >> Any input on this issue? >> >> Thanks in advance. >> >> >> _______________________________________________ >> 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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Phenix Xtriage label error
by Alex Lee 12 Apr '16

12 Apr '16

Dear Phenixbb members, I have a data-set of a 8 kDa protein crystal around 2.5A resolution. The protein crystal was soaked in potassium iodine before collecting data using in-house beam (1.54A wavelength). As I expected some anomalous signal from the iodine ion from the crystal, after I use Imosflm to index, integrate and scale the data (space group P3). I got four output .mtz files: pointless_XXX.mtz; aimless_xxx.mtz; ctruncate_xxx.mtz; ctruncate_xxx-unique.mtz. After I check with viewHKL, I found the only unmerged mtz data is pointless_XXX.mtz, the other three mtz files are merged. The next step I tried to use Phenix Xtriage (Linux version 1.10.1) to check my mtz data for anomalous completeness, I thought in this step my mtz should be unmerged type to see the anomalous signal, so I chose "pointless_xxx.mtz" as Xtriage input, but for the data labels in the Xtriage GUI panel, I can only have two choices of "I, SIGI, Merged" and "IPR, SIGIPR, Merged", it seems I do not have a choice of an unmerged mtz label. I decide to leave this choice blank by choosing data labels"---". After I click "run", Xtriage gave an error "please select labels for input data". Any input on this issue? Thanks in advance.

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Hardward phenix.refine
by Colin Levy 11 Apr '16

11 Apr '16

Dear all, Having read the FAQ regarding hardware I have a few ideas but would greatly appreciate any input from the community or developers. Would anyone like to suggest the best configuration of hardware for running phenix.refine? I mainly operate in OSX but have no issue with switching operating system if I can get a faster setup. My current thoughts are either something running a 4GHz Quad core i7 or an alternative would be a 3.7GHz Quad-Core Intel Xeon E5 (iMac v Mac Pro) or equivalent Linux builds. I know that the i7 is reasonably fast as I have this setup in a different machine and phenix.refine runs reasonably quickly but as ever I would like it to be faster. Budget is not unlimited by any means but I would be interested in learning what an optimal setup might look like. 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<mailto:[email protected]> Manchester Institute of Biotechnology | University of Manchester | 3.020 Garside Building | 131 Princess Street | Manchester | M1 7DN [cid:[email protected]]<https://www.facebook.com/MIB2006/?ref=aymt_homepage_panel>[cid:[email protected]]<https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/p…>[cid:[email protected]]<https://www.linkedin.com/company/manchester-institute-of-biotechnology?trk=…>[cid:[email protected]]<https://twitter.com/?lang=en-gb&lang=en-gb>[cid:[email protected]]<https://www.youtube.com/channel/UCCBV8zDxk4L9yOEcujvSFNw> <https://www.youtube.com/channel/UCCBV8zDxk4L9yOEcujvSFNw><https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/p…><https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/p…><https://plus.google.com/u/0/b/111834792186886067949/111834792186886067949/p…>

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Call for targets for CASP12 - Critical Assessment of Protein Structure Prediction
by Torsten Schwede 08 Apr '16

08 Apr '16

Dear colleagues, The CASP experiment is looking for prediction targets: Novel folds, membrane proteins, protein complexes and multimers, comparative modeling targets. As many of you know, the CASP community experiments have been running once every two years since 1994, collecting information on soon to be solved structures from the experimental community, and passing on sequence data to the structure modeling community so that blind predictions of structure can be collected and assessed. Over that period CASP has seen enormous progress in the quality of modeled structures, but many problems remain, and further testing of prediction methods is imperative for advancing the field. CASP organizers collect target information for a three month season every two years, and in that period we can acquire around 100 targets, sufficient to evaluate the state of the art for most types of modeling. For those of you who have not provided targets to CASP before, the procedure is simple - there is a web page for submitting targets, and a very experienced staff to deal with any queries. We don't need the structure in advance of its release by the PDB, and if we are notified early enough (a minimum of three weeks before release, more is better) there need be no delay in structure release. We need all sorts of targets and in general everything that has low coverage by the templates (<70% of the sequence length) and relatively low sequence identity to the best template (<50% ) will be appreciated. In particular, we are interested in: 1. Novel folds and membrane protein targets. Last round we observed some interesting methods developments for contact prediction and ab initio modeling, and it is important to be able to decisively evaluate their effectiveness this CASP again. 2. Protein complexes and multimers. Since the last edition of CASP, the assessment of structure prediction methods has stronger emphasis on evaluating the accuracy of quaternary structure prediction. Both oligomeric targets and complexes are of interest for the experiment. 3. A diversity of comparative modeling targets. Cases where there is fairly high sequence identity (30-50%) between the target structure and an available template are valuable for testing the degree to which model accuracy can approach that of experiment, particularly in functionally critical regions. Cases with lower sequence identity to template, right down to undetectable, are valuable for testing the ability of the methods to detect remote homologs, to overcome challenging alignment difficulties, to make use of multiple templates, and to build regions of the structure not obviously available from a template. The time table is similar to previous CASPs: The prediction season opens at the beginning of May, and will run until the end of July. We are releasing targets continuously throughout that period, as evenly spaced as possible, aiming for about 100 targets altogether. Each target will be available for prediction for a period of three weeks. For cases where longer periods are possible, these targets may be used to test refinement and data-assisted methods. It is of course important that there not be any kind of public release of the experimental structure (including things like pictures on web pages or abstracts) until after the predictions for that target are closed. As many of you know, it's fairly simple, with just two things to bear in mind. First, because of the timing framework, there needs to be at least a month between the submission date and any release of the structure. Second, we ideally need the experimental co-ordinates by the beginning of August and definitely by the end of August, so that the predictions can be assessed. At that point, they can be kept confidential if necessary, though we would like to provide them to predictors of your structure at the beginning of November at the latest, so that can see how well they have done. Participants would also usually like to be able to show slides and discuss their predictions at the meeting at the beginning of December. So, if you are currently working on an interesting protein structure suitable as prediction target for CASP , we would be most grateful if you would inform us via the target entry page: http://www.predictioncenter.org/casp12/targets_submission.cgi After CASP prediction season is over we usually publish a paper on the experimentalists' insights into the most interesting targets (see below). 2015: Some of the most interesting CASP11 targets through the eyes of their authors. Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T. Proteins. 2015 Oct 16. doi: 10.1002/prot.24942. [Epub ahead of print]. PMID: 26473983. 2014: Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. Proteins. 2014 Feb;82 Suppl 2:26-42. doi: 10.1002/prot.24489. Erratum in: Proteins. 2015 Jun;83(6):1198. PMID: 24318984. 2011: Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T. Proteins. 2011;79 Suppl 10:6-20. doi: 10.1002/prot.23196. Epub 2011 Oct 21. PMID: 22020785. Thanks, CASP organizing committee: John Moult, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, University of Basel, Switzerland Anna Tramontano, University of Rome, Italy Get in touch: casp(a)predictioncenter.org<mailto:[email protected]> More information: http://www.predictioncenter.org/casp12/index.cgi Submit a target: http://www.predictioncenter.org/casp12/targets_submission.cgi

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Position available with Phaser team at University of Cambridge
by Randy Read 06 Apr '16

06 Apr '16

I’d like to draw your attention to an opening that we have for someone to join the team developing Phaser. The ideal person would have experience with C++ and/or Python, graphical interfaces, and knowledge of how macromolecular structures are solved and validated, but it would also be good to hear from people who only tick some of those boxes. Full details of the position and the application process are given on the jobs.ac.uk website: http://www.jobs.ac.uk/job/ANJ468/research-associate/. I’m happy to answer any informal enquiries about the position. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Modeller- homology modelling
by Shilpa Janarthanan 03 Apr '16

03 Apr '16

Hello, Has anyone encountered this error while running Modeller for doing Homology modelling "Sequence mismatch between alignment and pdb"? If yes, how did you solve it? I checked, there is no mismatch between sequence(both fasta and pdb) and alignment. Thank you. -- Shilpa J Bioinformatics Dept., SASTRA University.

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Finding the transcript
by Shilpa Janarthanan 02 Apr '16

02 Apr '16

Hello, Can you tell me, on what basis should I find the exact transcript (mRNA) sequence for a given protein sequence, in NCBI -Gene? Thank you. -- Shilpa J Bioinformatics Dept., SASTRA University.

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The Hitchhiker’s Guide to the Biomolecular Galaxy symposium - May 11-12th 2016
by Noinaj, Nicholas 02 Apr '16

02 Apr '16

Dear PHENIXbb, I would like to bring to your attention our upcoming symposium (May 11-12) hosted here at Purdue University for students and postdocs. There will also be a Career Session on May 10th for students and postdocs only. More information is listed below and can also be accessed on our website: Symposium Website: https://purduegalaxy.science.purdue.edu/ Symposium Flyer: https://purduegalaxy.science.purdue.edu/images/2016/hg2bg_logo_Flyer_new.jpg Registration (including breakfast and lunch for both days and a T-shirt!) and abstract submission are completely FREE! And now, we are offering at least 10 travel grants (up to $150 each) for students and postdocs who are within driving distance of Purdue. Please forward this to anyone you think might be interested. 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) nnoinaj(a)purdue.edu ++++++++ Greetings all from Purdue! We would like to cordially invite you, your colleagues, students, postdocs and staff to our upcoming symposium hosted here at Purdue University, West Lafayette campus. The name of the symposium is: The Hitchhiker’s Guide to the Biomolecular Galaxy symposium May 11-12, 2016 ARMS 1010, Purdue University The symposium will highlight research from students and postdocs from neighboring institutions and from many departments here at Purdue including Biological Sciences, Medicinal Chemistry and Molecular Pharmacology, Chemistry, Biochemistry, and Physics and Astronomy. The keynote speaker will be Dr. Peter Kwong from NIAID/NIH who will talk about his work on ‘Multi-dimensional searching and the coordinates of effective HIV-1 and RSV vaccines’. In addition to the keynote address, the symposium will include six scientific sessions covering the following topics: Disease, Pathogenesis and Therapeutics; Biosynthesis and Catalysis; Biophysical Methods and Emerging Techniques; Macromolecular Assemblies and Complexes; and Disorder and Conformational Plasticity. There will also be opportunities for discussion and interactions during catered breaks, a poster session, and a reception. And back by popular demand, a Career Session will also be hosted on the evening of May 10th at the Lafayette Brewing Company for students and postdocs and will include a panel representing industry, academia, and government. Registration and abstract submission are both FREE. Undergraduates, graduates, and postdocs are encouraged to submit abstracts for poster or oral presentations. Prizes for best posters (undergrad ($100), grad ($150), and postdoc($150)) and oral presentations (grad ($200) and postdoc ($200)) will also be awarded at the close of the symposium. REGISTER NOW for the HG2BG symposium!!! The deadline is quickly approaching!!! Click link below to Register (Abstract submission NOT required!): https://purdue.qualtrics.com/jfe/form/SV_eeZ2HT409liD27z Just LOOK at ALL the FREE stuff you get with registration: Just a 1-click, 1-minute process FREE registration fees! FREE abstracts submission! FREE attendance to the Career Session which includes food and drinks at Lafayette Brewing Company! FREE HG2BG symposium T-shirt! FREE chance to win either a poster/oral presentation prize ($100-$200 each)! FREE food and drinks at the poster presentations/reception! FREE breakfast for both days of the symposium! FREE lunch for both days of the symposium! FREE travel grants for up to $150 each for registrants from neighboring institutions (10 available)! FREE attendance to all poster and oral presentations, including talk by Peter Kwong! We look forward to your participation and another successful symposium! On behalf of the organizing committee: Satarupa Bhaduri (Biological Sciences) Chen Chen (Medicinal Chemistry and Molecular Pharmacology) Samantha Lee (Biochemistry) Ngango Yvon Rugema (Chemistry) Phillip Rushton (Biological Sciences/ PULSe) Valentyn Stadnytskyi (Physics and Astronomy) Dr. Nicholas Noinaj (Faculty advisor; Biological Sciences) A special thanks to our corporate sponsors: Millipore(Jim Henderson) Carl Zeiss Microscopy LLC (Sam Byerly) Molecular Dimensions (Issa Isaac) Qiagen (Andrew Fritts) Rigaku (Angela Criswell) TTP Labtech (Melanie Adams) Anatrace (Ed Pryor) Hinds Instruments (Connie Wimmer) Beckman Coulter (Jona Kristo) Mitegen (Ben Apker) Fisher Scientific (Keven Peterson) Sigma Aldrich (Rick Belcher)

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