- phenixbb - phenix-online.org

phenix.resolve_cryo_em
by Reza Khayat 25 Aug '20

25 Aug '20

?Hi, I'm running into a clipping issue with phenix.resolve_cryo_em. The program seems to be improving the map; however, portions of the map get clipped. Any suggestion would be appreciated. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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MicroED Imaging Center
by Johan Hattne 24 Aug '20

24 Aug '20

Dear Structural biology community; We are delighted to announce that the National Institutes of Health is helping us establish a Biotechnology Development Research Center focused on MicroED at UCLA School of Medicine, named MicroED Imaging Center (MEDIC). The main thrust of MEDIC is for method development and research focused on MicroED. As part of community engagement, the center will host the annual MicroED course as well as an annual MicroED Summit, both of which will be staged at the UCLA School of Medicine, and open to the community on a first come first serve basis until spaces are filled. Approximately 90% of available spots will be allocated to academic attendees and 10% to industry attendees. This will be a continuation of almost 10 years of tradition of providing workshops and training to the community. Also, there is some opportunity for the community to collect data on MEDIC microscopes. There is also limited availability for one-on-one user training at the center at UCLA for microscope set up and data collection. Users and trainees will be invited based on replies to a call for proposals, which will be advertised shortly. The proposals will be reviewed by an advisory committee. Because of the COVID19 pandemic and the limitations on travel and hosting imposed by UCLA we cannot begin these activities at this stage. On a related note, UCLA School of Medicine is also running a MicroED Imaging Core which is open as a pay per use service for academia and industry. This activity is independent of the Gonen Lab and from the NIH funded research program on MicroED. Details can be found online. Kind regards Tamir Gonen and Pawel Penczek

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error while Auto sharpen
by sangeeta niranjan 19 Aug '20

19 Aug '20

Hello, I am trying to use Auto Sharpen feature of a CyoEM refined map into Phenix but the job is getting failed every time with the following error: Missing the model file: followed with model file name and location. Although it was working before but now it's showing the same error for all the auto sharpen runs including Models/PDBs. Thank you -- Sangeeta Niranjan Ph.D. Student, Lab of structural Biology Lab-6 NB National Centre for cell Science Ganeshkhind, Pune, India

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moving folders
by Thomas, Leonard M. 18 Aug '20

18 Aug '20

Hello, I know this come up every so often by my google-fu is sorely lacking to find the answer. How does one move a project folder? I have a project and not thinking things through set it up in the wrong folder. I would like to move the whole thing to another folder maintaining the project structure. Thanks, Len Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu<mailto:[email protected]> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

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Phenix.Refine fix WXC has no effect
by White, Mark 17 Aug '20

17 Aug '20

Hello, I am refining a 3.5 Å structure using the latest stable version of Phenix.Refine. After switching to the latest version the Bond RMSDs exploded to ~ 0.035 Å, when using optimize wxc. Turning off Optimize and using the "Fix WXC" parameters in the GUI with increasingly smaller values had almost no effect on the final bond rmsds, which seems to explode from reasonable values in the "3_xyz" step of refinement. Am I missing something? Best regards, Mark Mark Andrew White, Ph.D. Associate Professor of Biochemistry & Molecular Biology, Manager, SCSB Macromolecular X-ray Laboratory UTMB, Galveston, TX http://xray.utmb.edu

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Phenix.refine on coordinate-optimised structures
by Joey Farrell 08 Aug '20

08 Aug '20

Hello, I am trying to design a set of input parameters that I will be passing through the phenix.refine function. The structures that I am working with have already had their X,Y, and Z orthogonal Å coordinates optimised via separate protocol. I am looking for advice on which strategies and parameter values to use with phenix.refine to improve the crystallographic R-factors of such structures while preserving their earlier optimisation in real space. I have been having some success using “strategy = tls+individual_adp+occupancies” (where tls = “chain A”, tls = “chain B”, etc.) as well as adjusting the wxu_scale value until R-work and R-free are minimised. Are there other strategies or phenix.refine functionalities that may also prove helpful with this end in mind? I believe there may be ways to further improve R-work and R-free with this software that I am not yet aware of. Thank you for your help! Best, Joey

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Phenix Real_Space_Refine and Torsion NCS restraints
by Mark A. White 04 Aug '20

04 Aug '20

Hello, Are there plans to include Torsion Angle NCS restraints in the Phenix.Real_Space_Refine module? At low resolution (~ 3-4Å) I would like to include NCS restraints, but my molecule is flexible and the strict NCS constraints used in the Real_Space_Refine module are not appropriate. I am currently using phenix-1.18.2-3874. Best regards, Mark

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map to model - DNA model building
by Manoj saxena 04 Aug '20

04 Aug '20

Hello, I am trying to fit a cryo-EM map of a DNA protein complex (3.3 A) using the map to model in Phenix 1.18.2.3874, with a DNA sequence input in fasta format and the map as a .ccp4 file. However the output model fitted in the map I am getting is many fragmented PDB files and only one chain of DNA. What is the best way to get a higher fraction of the DNA model fitted into the map, can I switch off the segmentation of map and get both strands fitted into the map. Or the only option is to manually build? Thanks for your help Regards Manoj Saxena

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Model moving out of map
by Shanti Pal Gangwar 03 Aug '20

03 Aug '20

Dear all, I am trying to refine a Cryo-EM map at a decent resolution. The model was fit into the map in chimera and refined against the same map in Real space refinement in Phenix but after the run, a significant part of the model moved out of the density. I would appreciate any suggestion/strategy to solve this issue. Thank you Shanti Pal

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Postdoc position at UT Health Science Center, San Antonio, Texas
by Yogesh Gupta 03 Aug '20

03 Aug '20

The laboratory of Dr. Yogesh Gupta at University of Texas Health Science Center in San Antonio is seeking an enthusiastic Postdoctoral Fellow to study the structure and function of nucleoproteins in infectious diseases and cancer. We combine structural biology tools (X-ray, cryo-EM, NMR) with cell-based methods to address mechanistic questions and exploit this knowledge for drug development. Please visit below websites to learn about our research program – https://www.nature.com/articles/s41467-020-17496-8 *http://ccri.uthscsa.edu/YGupta.html <http://ccri.uthscsa.edu/YGupta.html>* Preference will be given to applicants with demonstrated experience in macromolecular crystallography. Candidates are expected to possess strong organizational, interpersonal skills, and ability to work as part of a team. An ideal candidate should hold (or soon expect to hold) a Ph.D. or equivalent degree in biochemistry/biophysics/structural biology and have no more than 2 years of postdoc experience. Salary is competitive. San Antonio offers affordable cost of living and there is no state income tax in Texas. If interested in applying, please send a short description of your research accomplishments, and CV with a list of 3 references to Dr. Yogesh Gupta (email: *guptay(a)uthscsa.edu <guptay(a)uthscsa.edu>*). The Greehey Children’s Cancer Research Institute is a unique specialized cancer research center focusing on basic and translational research in childhood cancer and occupies a state-of-the-art 100,000 sq. foot research facility on the university’s Greehey Academic and Research Campus. San Antonio is the nation’s seventh largest city and is located at the edge of the beautiful Texas Hill Country. San Antonio offers a rich, multi-cultural community, affordable cost of living, excellent weather and a thriving biomedical industry.* All Postdoctoral appointments are designated as security sensitive positions. The University of Texas Health Science Center at San Antonio is an Equal Opportunity/Affirmative Action Employer including protected veterans and persons with disabilities.* Thank you very much for your time. Yogesh -- Yogesh Gupta, PhD Assistant Professor of Biochemistry & Structural Biology PI, Greehey Children's Cancer Research Institute University of Texas Health Science Center 8403 Floyd Curl Drive, San Antonio, Texas, USA 78229 http://ccri.uthscsa.edu/YGupta.html

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