Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol
Thank you Bernard. I'd like to add that carving the density shown in a figure (especially without explicitly describing the carve radius used) is the moral equivalent of showing only 1mm of background above and below the band of interest in a western blot. Phoebe From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard Rupp [hofkristall...@gmail.com] Sent: Tuesday, March 21, 2017 3:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol > and carve=2.0 means the mesh is created within 2.0 Å of the selected atoms. > Adjust these values to suit. I would advise extreme care when employing such presentation features. They are useful for display purposes and only when their use is stated as such, but they also open a venue for cognitive biases. One might want to have a look at how creative use of these ‘blob’ features until things ‘suit’ can betray the true believer… http://www.ruppweb.org/cvs/br/rupp_2001_NSB_questions_BotA.pdf https://www.dropbox.com/s/iul2cjbuu4x2o9f/Hanson_2009_retraction_bot_nsmb0709-795.pdf?dl=0 Best, BR The first principle is that you must not fool yourself and you are the easiest person to fool.” Richard P. Feynman
[ccp4bb] Opening for a PhD position
Dear All, There will be an opening for 1 PhD position (starting date: June 2017) in my group at the LOEWE Center for synthetic Microbiology (SYNMIKRO) at the Philipps University Marburg, Germany. SYNMIKRO is a highly interdisciplinary center that consists of members from seven faculties of the university of Marburg and the four departments of the local Max Planck Institute. Drawing on Marburg’s highly-rated expertise in microbiology, it integrates almost 30 laboratory groups at the university and the Max Planck Institute to cover all aspects of microbial life from the molecular level to whole cells and communities. The project involves a multidisciplinary approach to understand the control of the bacterial metabolism by nucleotide-based second messengers in response to stress and environmental changes (Check: Steinchen et al., 2015, PNAS; Steinchen & Bange, 2016, Molecular Microbiology). The PhD research projects will foster skills in cell biology, protein biochemistry, automated hydrogen-deuterium exchange massspectrometry (HDX), X-ray protein crystallography and cryoEM. Further information can be found at: www.bangelab.org Please send your letter of interest including a CV and the names of three referees as a single pdf document to: g...@bangelab.org. With best regards, Gert - Philipps-University-Marburg LOEWE Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry Dr. Gert Bange Hans-Meerwein-Strasse, C7 35043 Marburg, Germany office: +49-6421-28-23361 web: www.bangelab.org Twitter: @BangeBalcony
[ccp4bb] tNCS and PISA
I am turning again to the wisdom of the community. In a paper, the authors used a dataset in P 1 2(1) 1 displaying tNCS (not mentioned anywhere in the paper) to model a dimeric structure. At the refinement stage, they used a twin law. Looking at the PDB-REDO entry, there is a warning line - "Used extra refinement runs to compensate for possible R-free bias". When I ran the data from PDB in Xtriage, I get the following: 1. translational NCS is present at a level that may complicate refinement 2. severe anisotropy (is this unsurprising because when I re-refined it, the CCwork/free didn't display a classical drop at the high resolution? artificial truncation?) 3. one or more twin operators show a significant twin fraction but since the intensity statistics does not indicate twinning, you may have an NCS rotation axis parallel to crystallographic axis 4. one or more symmetry operators suggest that the data has a higher symmetry 5. the intensity statistics look normal, indicating the data are not twinned. How should I proceed in re-refining this structure? Reindex to P222 and re-do molecular replacement? The reason I am interested in this model is that the authors claim their structure is a homodimer but PISA deltaG(diss) is around 4 kcal/mol. In a related structure where the protein was co-crystallized with another protein, the homodimer deltaG(diss) is about 7. Is this a significant difference? Thanks. Mohamed
[ccp4bb] MoRDa update
Dear All Morda at ccp4online has been updated. The structure solution program is improved and database is extended by about 900 entries. The update is also available for existing local Morda installations and can be installed from command line: change to installation directory (by default MoRDa_DB) and type ./update_morda. Both update and installation instructions are available from Morda homepage. Best regards Alexey
[ccp4bb] Research Fellow Position available in Institute of Molecular and Cell Biology, Singapore
Dear All, We are seeking an enthusiastic and self-motivated postdoctoral research fellow to work on structural and functional analysis of proteins involved in RNA metabolism and the Hippo signalling pathway. The applicants should have a background in structural biology, biophysics, biochemistry or a related field with a strong publication record. Candidates with experiences in structure determination by cryo-electron microscopy or in protein expression using insect/mammalian cells are preferred. Please send CV, including the names and addresses of three references to: Prof. Haiwei Song Institute of Molecular and Cell Biology 61 Biopolis Drive Proteos Singapore 138673 Email:hai...@imcb.a-star.edu.sg. http://www.imcb.a-star.edu.sg/php/shw.php
Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol
> and carve=2.0 means the mesh is created within 2.0 Å of the selected atoms. > Adjust these values to suit. I would advise extreme care when employing such presentation features. They are useful for display purposes and only when their use is stated as such, but they also open a venue for cognitive biases. One might want to have a look at how creative use of these ‘blob’ features until things ‘suit’ can betray the true believer… http://www.ruppweb.org/cvs/br/rupp_2001_NSB_questions_BotA.pdf https://www.dropbox.com/s/iul2cjbuu4x2o9f/Hanson_2009_retraction_bot_nsmb0709-795.pdf?dl=0 Best, BR The first principle is that you must not fool yourself and you are the easiest person to fool.” Richard P. Feynman
