- phenixbb - phenix-online.org

Appropriate model_vs_data usage over part of a structure
by Andy Watkins 26 May '16

26 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 24 May '16

24 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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