[ccp4bb] Atom clashes in active site?
Hi all, I have a structure of a condensing enzyme with substrate bound. The active site is very tight, requiring some of the substrate atoms to clash with a catalytic cysteine. This means that although the substrate fits the density nicely upon manual real-space refinement, phenix recognises the clash, resulting in the displacement of substrate atoms so that they are outside the density. I can mostly fix this by using distance restraints, but I'd rather allow it to refine in a less biased manner, but ignore the clash. Is this a acceptable way forward? If so, is there a parameter I can edit to tell phenix to ignore clashes between these specific atoms? Thanks, Andrew Marshall PhD Candidate Laboratory of Protein Crystallography Dept. of Molecular and Cellular Biology School of Biological Sciences The University of Adelaide
[ccp4bb] A Postdoctoral fellow positions available in biochemistry and structural biology
A postdoctoral fellow position is available immediately in the Department of Molecular and Structural Biochemistry at North Carolina State University for Biochemistry and/or protein crystallography. Research in our lab focuses on structural elucidation of protein kinases in cellular signal transduction. We convene an interdisciplinary approach to tackle the underlying questions that includes X-ray crystallography, biochemistry, biophysics, cell biology and in vivo analyses. http://biochem.ncsu.edu/faculty_list.php http://biochem.ncsu.edu/faculty/guozhou/guozhoupage.php https://biochem.ncsu.edu/faculty/guozhou/www/XuLabStaticWebApp/WebContent/htmls/index.html Candidates should be motivated to work independently. The selected postdoc will have the opportunity to conduct research in a truly interdisciplinary setting with close interactions with Biochemistry, Molecular biology and Structural biology groups. Candidates with expertise in at least the following areas are invited to apply: - Extensive experience in molecular cloning and protein purification. - Experience in working with X-ray crystallography is preferred. In addition, candidates are required to demonstrate excellent written and verbal communication skills. Interested candidates should email their full CV and a list of three references. NC State University (NCSU) is one of the prestigious public universities in US. It is located at the center of North Carolina’s Research Triangle Area, which has multiple research, medicinal, healthcare institutes and biomedical industries. There are ample career opportunities in Biotechnology and medicine. In addition, research triangle area is one of the best places in US for living. Raleigh-Durham area has a lower living cost compared to other big cities. However, quality of living, education, healthcare is among one of the best in the nation. Contact information: Guozhou Xu, PhD Assistant professor of Biochemistry Department of Molecular and Structural Biochemistry North Carolina State University Raleigh, NC 27695-7622 Phone: 919-515-0835 (Office) or 646-645-9121 (Cell) E-mail: g...@ncsu.edu
[ccp4bb] SPHIRE beta release
Dear EM-community, We are happy to bring our new software package SPHIRE to the world of cryo-EM. We announced SPHIRE (SParx for HIgh Resolution Electron Microscopy) at this year’s GRC conference in Hong Kong and, in response to the interest of the community we deliver now the early version of the package. SPHIRE embodies a single-particle pipeline supported by ten modules of the previous SPARX system that are accessible through an easy-to-use GUI (Graphical User Interface). It is designed for easy immersion into cryo-EM with the stress on validation and reproducibility of results by using concepts of statistical resampling and provides powerful algorithms that encompass all steps of a typical cryo-EM project. Advanced users have the luxury of easy access to all process parameters through ‘advanced’ tabs and can easily customize the code, which is written in transparent Python! THE TESTS During the last months we worked day and night to extensively test the workflow. We used our in-house datasets and also processed a number of EMPIAR datasets (e.g. TRPV1 (ID: 10005), T20S proteasome (ID: 10025), beta-galactosidase (ID: 10061)) and are happy to report that in all cases we were able to reproduce published results. The SPHIRE pipeline comprises the following major steps: - Frame movie alignment, supported by a graphical drift assessment tool. - CTF estimation and its error assessment tool providing utilities for automated sorting out of inferior data. - Reproducible 2-D classification. - Validated ab initio 3-D reconstruction yielding a perfect starting point for 3-D refinement. - Efficient 3-D structure refinement utilizing maximum likelihood methodology. - Tools for assessing data heterogeneity, including computation of local variance, local resolution providing the necessary validation for our 3D sorting program. THE INFO To find out more about SPHIRE and its team please consult http://sphire.mpg.de The SPHIRE team is accessible almost 24/7 via mailing list. To subscribe please visit: https://listserv.gwdg.de/mailman/listinfo/sphire where you can also browse through the archive of already discussed subjects. In order to facilitate smooth immersion into the SPHIRE world, we prepared an extensive step-by-step tutorial that is supported by a test dataset. Both can also be downloaded from the SPHIRE homepage. THE RELEASE And now the most important part, the release. We have decided to release SPHIRE as a public beta version and here is why: Despite the substantial testing, as a developer team we are only able to test a limited number of datasets so it is reasonable to expect the unexpected. We hope for the community input that will allow us to find problems we did not anticipate and solve them quickly. This phase will be followed by a stable release of SPHIRE within the next year. THE FUTURE We believe that increasing the number of cryo-EM software packages will benefit our community by providing alternative solutions to challenges of cryo-EM structure determination. We sincerely hope SPHIRE will meet your expectations. More importantly, we hope for community feedback, however enthusiastic or critical it may be, to stimulate us for the future developments to carry us into the next quarter of the century. Your SPHIRE development team [cid:D58434BF-44E4-43F0-81A3-928977BCAE42@client.mpi-dortmund.mpg.de]
